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The Lookback Period Mistake That Turns Valid Refunds Into Permanent Losses

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Lenora Hamilton thought she had everything figured out. She filed her 2017 tax return in November 2021—late, but still claiming a $2,070 refund she believed was rightfully hers. The IRS immediately rejected her claim. She appealed, lost, and spent nearly a year fighting in federal court.

The final verdict in early 2025 delivered a crushing blow: the court ruled her claim was “timely filed,” but she couldn’t recover a single dollar. Not because the refund was wrong, but because she missed something called the “lookback period.” A technical timing rule had permanently erased her entire refund.

In a recent episode of the Tax in Action podcast, host Jeremy Wells used Hamilton’s story to explain the refund statute of limitations—a subject most tax professionals think they understand but actually don’t. The stakes are enormous: once these deadlines pass, Wells warns, “there’s virtually no going back.”

The Two-Step Framework That Trips Up Even Experienced Practitioners

Most tax professionals think the refund statute of limitations is straightforward. File within three years, get your refund. But Wells explains it’s a complex two-step process where each step has different rules and different consequences.

Step One: Can You File at All?

The first step determines whether you can file a refund claim. This “limitation period” is the later of either three years after the return was filed or two years after the tax was paid if no return was filed. Wells calls this the “refund statute end date,” and it’s your final deadline to file any claim.

Here’s the key detail that trips up practitioners: “The filing of an original return, not an amended return, begins the period of limitation,” Wells explains. This means if you amend a return filed years ago, you’re still working within the timeline set by that original filing date.

Step Two: How Much Can You Actually Get?

Even if you file a timely claim, step two determines how much you can recover through the “lookback period.” The rules change dramatically based on when you file:

  • File within three years: You can look back at the full three years
  • File after three years: Your lookback period shrinks to just two years

This is where Hamilton got trapped. The court found she filed a timely claim, satisfying step one. But because she filed her 2017 return so late—November 2021—her lookback period couldn’t reach back to her 2017 tax payments, which were deemed made on April 15, 2018.

As Wells puts it, “The court said she filed a timely claim for refund. However, for that timely claim, there was no refund available. What does that mean? How can that be?” To understand the answer, you have to know when the IRS considers payments “made” under tax law.

The Payment Timing Trap That Caught COVID-Era Taxpayers

The lookback period depends on when payments are “deemed made,” not when they actually happened. This creates counterintuitive situations that can permanently cost taxpayers money.

The Withholding Rule

Under IRC section 6513, all tax withheld from your paychecks during the year is deemed paid on April 15th of the following year. It doesn’t matter if the money was withheld in January or December—it’s all considered paid on April 15th.

For Hamilton, “Her 2018 withholding is deemed paid on April 15th, 2019, which is the 15th day of the fourth month following the close of that tax year.”

The COVID-19 Disaster

These timing rules created a perfect storm during the pandemic. The IRS postponed filing deadlines—2019 returns were due on July 15, 2020, and 2020 returns were due on May 17, 2021. But payments were still deemed made on April 15th of each year.

This trapped taxpayers who filed during the postponement periods. Someone who filed their 2019 return on July 15, 2020 (perfectly timely) might wait until July 15, 2023, to file a refund claim. Their three-year lookback would run from July 15, 202,3 back to July 15, 2020. But their 2019 payments were deemed made on April 15, 2020, which falls outside their lookback window.

Wells explains: “This left taxpayers who didn’t file extensions for those tax years stuck with potentially valid refund claims, yet they didn’t have any periods within the lookback period because those payments were still deemed filed as of April 15th.”

The IRS eventually provided relief through Notice 2021-21, but only after recognizing that its own timing rules created harsh consequences for taxpayers who did nothing wrong.

The Dangerous “Due Date” Myth Costing Taxpayers Money

A destructive misconception in refund statute law sounds perfectly reasonable: “You have three years from the due date to claim a refund.” 

But Wells makes it crystal clear that this perception isn’t accurate. “The end date is actually three years from the filing date or possibly two years from the payment date.” The due date might coincide with these periods for taxpayers who file on time, but it’s not what controls the deadline.

Why the Due Date Myth Fails

The due date myth crumbles in the exact situations where practitioners need precision most:

  • Late-filed returns: A taxpayer who files their 2020 return in September 2023 doesn’t have until April 15, 2024 to claim refunds. Their three-year period starts from September 2023.
  • Amended returns with post-deadline payments: Wells explains these create situations where “a valid refund claim made more than three years after the due date, could look back into those payments made after the deadline.”

The Hamilton case perfectly illustrates this. If you applied the due date myth, you’d think she was too late filing in November 2021 for a 2017 return. But the court found her claim was timely because the real rules don’t work that way.

The Professional Liability Risk

For tax professionals, relying on the due date myth creates serious liability exposure. When practitioners give advice based on this oversimplified rule, they risk costing clients money they can never recover.

Wells emphasizes the finality built into these rules: “Once that statute of limitations is up, once you have passed that refund statute end date, there is no going back with some very, very limited exceptions.”

Why These Rules Are So Unforgiving

The refund statute of limitations operates with mechanical precision, regardless of hardship or apparent unfairness. Courts consistently rule that these deadlines are clear and unambiguous, so there’s no room for equitable exceptions or reasonable cause relief.

The Finality Principle

Congress built finality into the tax code intentionally. As Wells explains: “There’s an implicit concept in the tax code that Congress has written into it. I tend to call it finality.” At some point, taxpayers should feel confident that old tax years are truly closed.

But this finality only works if practitioners understand the real rules. The Hamilton case, with its modest $2,070 refund that became a years-long legal battle, shows how even small amounts trigger the same unforgiving rules that govern million-dollar refunds.

The Stakes for Tax Professionals

These rules affect every practitioner who works with amended returns, late filers, or clients with potential refund claims. Understanding when the IRS deems payments made, how postponements interact with lookback periods, and when the due date myth doesn’t apply isn’t just technical knowledge—it’s client protection. And it can be the difference between recovering thousands of dollars and losing them forever.

When Time Runs Out, Money Disappears Forever

The refund statute of limitations represents tax law at its most technically demanding and unforgiving. The two-step framework of limitation periods and lookback periods creates a system where understanding timing rules can mean the difference between financial recovery and permanent loss.

For tax professionals, these rules represent the intersection of expertise and fiduciary responsibility. Relying on oversimplified rules or misunderstand the distinction between filing dates and due dates means risking giving advice that permanently costs clients money.

This finality places enormous responsibility on practitioners to understand and navigate these rules correctly.

Don’t let technical complexity cost your clients money they can never recover. Listen to Wells’ complete Tax in Action episode to master these critical timing rules and protect your clients’ interests and your professional reputation.

The R&D Credit Reality Check Every Tax Professional Should Understand

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Picture this: A small business owner walks out of a networking event buzzing with excitement. Someone just told them about the Research and Development tax credit. They’re already mentally calculating how much they’ll save on the custom software they’ve been developing for their consulting practice.

This scenario happens all the time, and it shows the gap between what business owners expect and what the tax code actually delivers. In this episode of Tax in Action, host Jeremy Wells, EA, CPA, breaks down one of the most misunderstood areas of tax law: the Section 41 Research and Development Credit.

The Credit That Sounds Simple But Isn’t

When clients first hear about the R&D credit, they focus on that appealing 20% credit for increasing research activities. It sounds straightforward: spend money on research, get 20% back as a tax credit. But as Wells explains, this credit is much more complex.

“I work with a lot of small service-based businesses,” Wells says. “So it doesn’t come up a lot in my practice, but there have been some cases where we’ve had businesses qualify for the credit, and that’s always a little exciting for me.”

That excitement comes after navigating through layers of complexity that immediately separate hopeful applicants from actual recipients.

Section 41 actually has three different parts: qualified research expenses, basic research payments, and Energy Research Consortium credits. For most businesses, only the first part matters. The basic research component applies to research without specific business goals, which Wells dismisses for his small business clients. “If they don’t have a business goal, they probably are not going to be able to afford to pay me for very long.” The energy research component targets massive global energy companies, not typical clients for most tax professionals.

Here’s where the “20% credit” gets misleading. It’s not 20% of research expenses. It’s 20% of the excess of qualified research expenses over a “base amount.” This base amount calculation is complex, but for most businesses, it defaults to 50% of qualifying research expenses.

Wells breaks down the math: “In general, we’re looking at 50% of qualified research expenses and then we’re taking 20% of that.”

The result? What sounds like a 20% credit actually delivers roughly 10% of qualifying research expenses as an actual tax benefit.

But even this 10% assumes businesses can navigate the qualification requirements, which proves much harder than the math.

The Science Requirement That Trips Up Most Businesses

The real barriers come from qualification requirements that act like scientific gatekeepers. Wells identifies the core problem: “This is probably the strongest limitation on what qualifies for research relevant to my clients. The research has to involve a process of experimentation that relies on the principles of either the physical or biological sciences, engineering or computer science.”

This creates an immediate disconnect. When most business owners think about research and development, they think of any effort to improve their operations: better customer service, more efficient workflows, or custom software. But Section 41 demands genuine experimentation rooted in hard sciences.

The “process of experimentation” adds another hurdle. Wells explains that this process “evaluates one or more alternatives to develop or improve a business component where the result was uncertain.” This isn’t about having a clear goal and executing a known path—that’s implementation, not research. True qualifying research requires genuine uncertainty about whether proposed alternatives will work, plus systematic testing of multiple approaches.

This eliminates entire categories of business activities that feel innovative but don’t meet the technical standards. Market research, customer satisfaction studies, workflow optimization, and business process improvements all fall outside the boundaries. As Wells states, “If your research consists of trying to understand your customers better, that’s not going to qualify as research.”

Software development faces even tougher standards. Internal software must pass what Wells calls “a very high bar” through the high threshold of the innovation test. This test requires proof of “substantial and economically significant” improvements, backed by “significant economic risk” where the business commits “substantial resources” with genuine uncertainty about recovery.

The economic risk part proves particularly challenging for small businesses because it excludes what Wells calls “sweat equity.” He explains, “What doesn’t count here, is that sweat equity, or the time spent by the business owner, or the uncompensated work by their partners, or even their staff.”

This requirement for actual cash rather than time investment doesn’t align with how most small businesses operate. The solo consultant developing custom software or the manufacturing business owner optimizing processes typically invest primarily time and expertise rather than substantial cash. Under Section 41, this automatically disqualifies them.

Making It Work: Expenses, Strategies, and Professional Help

For businesses that navigate the scientific requirements, the wage allocation requirements immediately complicate things for any business hoping to qualify through employee efforts.

Wells explains the 80% rule: “If you’ve got some sort of support staff spending at least 80%, four out of five working days a week directly involved in that research project, then their wages qualify in full.” Anything less than 80% requires careful splitting between research and non-research activities.

This gets trickier with executives. Wells has seen businesses try to claim big portions of C-suite wages for research. However, even technical CEOs who contribute to research projects rarely abandon their executive duties entirely. Wells says practitioners must “look at bifurcating, if not entirely writing off, their wages and salaries as not related to the actual research project itself.”

For businesses without internal research capacity, contract research offers an alternative, though with percentage limitations that reduce the effective credit rate. The general rule allows only 65% of contractor payments to qualify, though this increases to 75% for qualified research consortia and 100% for eligible small businesses, universities, or federal laboratories.

Wells breaks down the math for businesses relying entirely on contractors. “If all the qualifying research expenditures are paid to contractors, then we only get about 6.5% of those expenditures in terms of the credit.”

Despite this reduced rate, Wells suggests the contractor route might be easier than internal allocation headaches. “It might also be more advantageous to pay contractors and be able to take 65% of what’s paid to contractors than to worry about taking existing staff and trying to allocate some of their work toward the research project.”

Wells also highlights the payroll tax election as a cash flow strategy for startups. Rather than waiting years to use R&D credits against income taxes, businesses can elect to apply credits against the employer’s 6.2% Social Security tax, creating immediate benefits.

Given all this complexity, Wells strongly recommends working with specialists. “Finding a good, reputable firm to work with or to recommend and refer your clients to. But in general, it’s important that you understand the basis and the basics of section 41.”

Busting Common Myths

Wells addresses two common misconceptions about the R&D credit.

First, that service businesses automatically don’t qualify. While most service businesses won’t qualify for traditional reasons, Wells suggests this shouldn’t lead to automatic dismissal. “It might be possible to advise them in such a way to help them qualify for it, at least in part.” This might involve outsourcing research to qualified contractors, developing products for eventual sale rather than purely internal use, or ensuring research projects involve genuine experimentation rather than predetermined paths.

Second, that payroll is required. Wells points out that contract research expenses can qualify, even if at reduced percentages. While the effective rate drops for businesses using only contractors, “that might be better than nothing,” and “better than thinking that it has to be payroll and therefore nothing qualifies.”

The Bottom Line for Tax Professionals

The Section 41 R&D credit shows how well-intentioned tax policy is accessible primarily to those with sophisticated professional guidance. What sounds like a straightforward “20% credit” turns into a technical challenge that eliminates most hopeful applicants.

For tax professionals, understanding complex credits isn’t just about technical knowledge; it’s about managing client relationships and setting appropriate expectations. The practitioner who dismissively tells clients they don’t qualify without understanding restructuring possibilities doesn’t serve the client well. But the advisor who raises false hopes by oversimplifying requirements creates bigger problems.

Listen to the full episode of the Tax in Action podcast for Wells’ full breakdown of Section 41. His practical approach helps practitioners distinguish between realistic opportunities and unrealistic expectations while serving clients’ best interests.

The R&D credit may be complicated, but understanding its complexities opens doors to legitimate opportunities.

The Legal Default Every Tax Pro Gets Backwards About Married Filing Status

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Your tax software automatically defaults to “Married Filing Jointly” the moment you indicate a client is married. Your training taught you that joint returns almost always produce better tax outcomes. Your clients assume that filing together is not just preferred, but somehow more “correct” than filing separately.

Here’s what most practitioners miss: the legal hierarchy works in reverse of what we assume.

This insight comes from Jeremy Wells on his Tax in Action: Practical Strategies for Tax Pros podcast, where he walks through one of the most misunderstood areas in tax practice. The reality? Filing separately isn’t the alternative—it’s the legal default under the tax code. Joint filing is an election under Code Section 6013 that requires both spouses’ explicit consent. If either spouse refuses, both must file separately, period.

While tax software defaults to married filing jointly and most practitioners assume it’s always the better choice, understanding the actual legal framework changes how you approach married clients—especially when non-tax factors create situations where paying more in taxes delivers better overall financial outcomes.

Understanding the Legal Framework Behind Filing Decisions

The foundation of smart filing decisions starts with grasping what the law actually says versus what practice assumes. Code Section 6013 doesn’t make joint filing automatic. It allows couples to “jointly elect” to file together if both spouses agree.

“Filing separately is actually the default,” Wells says. ”If it weren’t for code section 6013, we would have all married couples filing separate returns.” Without this specific code section creating the joint filing option, every married person in America would file individually.

Yet tax software creates false defaults that completely reverse this legal structure. The moment you indicate a client is married, the software assumes joint filing “to the point at which we have to backtrack whenever a situation comes up that might lead us to consider filing separate returns instead.”

This backward approach means we assume joint filing is normal and treat separate filing as the exception that needs justification. But legally, it works the other way around. Joint filing is the special election that both spouses must actively choose.

Wells explains, “The joint return, although it tends to produce the better result from a tax perspective, isn’t the default.” The better tax result doesn’t automatically make it the legal starting point.

Understanding this legal framework becomes crucial in situations involving financial disagreement, pending divorce, or simple disagreement between spouses. One spouse cannot force the other into a joint return, and that protection exists precisely because the law treats separate filing as the baseline position.

This legal reality also affects how you approach client conversations. Instead of asking “Why would you want to file separately?” you might ask “Do you both want to elect joint filing?” It’s a subtle shift that acknowledges the actual legal structure while opening space for clients to express concerns they might not otherwise voice.

The Tax Code’s Systematic Push Toward Joint Returns

Understanding why the tax code penalizes separate filers reveals both the logic behind joint filing’s popularity and the threshold where those penalties become acceptable costs for better overall outcomes.

The most immediate impact comes through tax rates and brackets. “Tax rates tend to be lower on a joint return,” Wells explains. Separate return brackets are higher but also smaller, meaning “more income being taxed at lower marginal rates” on joint returns, creating “a relatively lower effective rate across the returns.” For many couples, this difference alone can mean several thousand dollars in additional taxes when filing separately.

But the real penalties come from eliminating or restricting credits and deductions. The earned income credit, American Opportunity credit, and lifetime learning credit simply disappear for separate filers. Other credits have their income limitations cut in half. For example, the child tax credit and retirement savings contributions credit phase out at income levels that are 50% of joint return thresholds.

The Roth IRA contribution restriction is perhaps the most puzzling example. “Contributions to Roth IRAs are phased out for a modified AGI of just $10,000 for separate returns,” Wells notes. “This, honestly, is one of the provisions that really just confuses me… I’m not really sure what the justification for that is.” The practical effect? Most working couples filing separately simply cannot contribute to Roth IRAs at all.

Wells points out other significant restrictions. The state and local tax (SALT) cap drops from $10,000 for joint filers to just $5,000 for separate filers, even though single filers get the full $10,000 cap. The capital loss deduction gets cut in half from $3,000 to $1,500, and the student loan interest deduction disappears entirely for separate filers.

The “itemization trap” creates another layer of complexity. If one spouse itemizes deductions, the other spouse must also itemize—they cannot claim the standard deduction. This creates challenges when his firm prepares a return for one spouse but cannot get information about the other spouse’s filing decisions. “If we just don’t know, then we go with the approach that is most advantageous to the taxpayer we’re working with. But we issue a strong caveat.”

These disadvantages create what Wells calls a “preference” toward joint filing that has become so assumed that practitioners often don’t consider separate filing until specific problems arise. Yet understanding these penalties helps identify situations where accepting them delivers superior overall results.

When Separate Filing Makes Financial Sense

The mark of sophisticated tax practice isn’t finding the lowest tax liability; it’s delivering the best overall financial outcome for clients. Sometimes that means recommending the higher-tax option.

“Our job as tax professionals is not always to prepare the simplest, most tax-efficient return possible… Sometimes, our job is to advise the taxpayer on the options and tradeoffs and help them achieve the best overall result for their personal and financial needs.”

Student loan income-based repayment plans drive most separate filing decisions in modern practice. “Nine out of ten times when we file married filing separate returns in our firm, it’s because of student loan income-based repayment plans,” Wells says. These plans calculate monthly minimums based on the borrower’s tax return income. File jointly with a high-earning spouse, and those monthly payments can become unaffordable.

The financial impact often dwarfs any tax savings from joint filing. When one spouse owes substantial student loans while the other earns significant income, filing separately might increase taxes by $2,000 but reduce annual loan payments by $6,000, creating a net benefit of $4,000 for choosing the “higher tax” option.

Wells addresses practitioner hesitation about this strategy: using filing status as a tool to achieve a financial goal is completely legitimate. It absolutely is proper tax planning, he emphasizes. There’s no ethical concern, no audit risk, no regulatory problem. It’s smart financial planning that considers the complete picture.

Financial protection scenarios create another category where separate filing is advantageous. When couples face “disagreement, mistrust, or even financial abuse,” separate filing is about financial survival and legal protection.

Both spouses on a joint return become “jointly and severally liable for the tax liability,” meaning either spouse can be held responsible for 100% of any tax debt. This remains true even after divorce. IRS collection efforts don’t respect divorce decree assignments of tax liability because the IRS was never a party to that agreement.

Treasury offset protection is another practical application. When one spouse defaults on student loans, the federal government can garnish the entire joint refund to pay that debt. “Filing separately could protect that spouse’s refund… Getting some of that refund with a separate return could be a better result than having the entire refund garnished by the student loan lender,” Wells explains.

Separate filing may also unlock better results for AGI-limited deductions. The 7.5% AGI threshold for medical expenses is much more achievable when calculated against one spouse’s lower individual income rather than the couple’s combined AGI. Wells notes this same principle applies to casualty losses at 10% of AGI.

“Tax filing status is never a reflection of the couple’s marriage or relationship,” Wells explains, countering clients’ concerns that separate filing might signal relationship problems. “There’s nothing wrong about filing separate returns. Nobody looks at separate returns and thinks that’s an indication of something wrong with your marriage.”

Professional Implementation and Practice Management

The realities of implementing separate filing strategies reveal professional challenges beyond tax calculations. Wells shares insights from his firm’s experience that help practitioners navigate these complex decisions effectively.

One fundamental challenge involves timing and irrevocability. Wells explains the common saying, “A couple can make up, but they can’t break up.” Once you file jointly and pass the filing deadline, you generally cannot switch to separate returns. However, the reverse is possible. Separate filers can amend to joint returns within the statute of limitations.

There are limited exceptions to this rule. Couples can file a superseding return before the unextended due date to switch from joint to separate. They can also amend joint returns to separate if the marriage gets annulled, if one spouse can prove the joint return was signed under duress, or if both taxpayers didn’t properly sign the joint return. However, these exceptions require a substantial legal burden of proof.

Technology can streamline the analysis process, as professional tax software includes joint versus separate worksheets. These comparison tools show four columns: the joint return result, each spouse individually as if filing separately, and the combined result of two separate returns. “Usually it’s not an insignificant amount of money. A lot of times we see several thousand dollars” in savings from joint filing, Wells notes.

Wells uses these worksheets for quality control. “That comparison can actually help work through whether or not we’ve made an error.” For example, if all wages show under one spouse and none under the other, it might indicate misallocated W-2s that could incorrectly trigger Social Security overpayment calculations.

Wells describes a specific error his firm caught this way. “I have mislabeled those W-2s and that’s triggered a calculation of that excess Social Security tax paid.” Since Social Security overpayment calculations work on an individual basis, not a joint return basis, misallocating W-2s between spouses can create incorrect refund calculations that later generate IRS notices.

Conflict of interest considerations are crucial when working with couples contemplating separation or divorce. “Working with a married couple that is on the rocks might cause a conflict of interest, especially if the firm started working with one spouse before the couple got married,” Wells explains. Some firms require written waivers, while others simply refuse to work with both spouses during contentious situations.

Different firms handle separate filing preparation differently. Wells notes that some treat separate returns as completely independent engagements with separate fees for each spouse. Others charge for three returns when preparing both joint and separate scenarios. The key is establishing clear policies before these situations arise.

Transforming Client Relationships Through Strategic Tax Planning

The separate filing decision is sophisticated tax practice at its best, where technical knowledge meets strategic thinking to deliver advice that considers clients’ complete financial circumstances rather than just tax calculations.

Wells’ approach demonstrates how understanding these concepts transforms client relationships. Instead of simply optimizing tax calculations, you help clients navigate complex financial decisions that affect their long-term financial health. You become the advisor who understands that sometimes paying more in taxes is the smartest financial move.

Client education is crucial for successful implementation. Wells often encounters clients who resist separate filing because they believe it signals relationship problems or creates complications. Having clear, confident responses to these concerns, backed by a solid understanding of the legal framework, positions you as the expert who can cut through confusion.

“Our job as tax professionals is not always to prepare the simplest, most tax efficient return possible,” Wells says. “Sometimes, our job is to advise the taxpayer on the options and tradeoffs and help them achieve the best overall result for their personal and financial needs.”

This philosophy requires moving beyond traditional tax optimization to consider complete financial circumstances. When you can save a client thousands in student loan payments by recommending separate filing (even while paying extra taxes), you’ve delivered genuine strategic value that differentiates sophisticated tax professionals from basic return preparers.

The separate filing decision crystallizes everything that makes tax planning both challenging and valuable: technical complexity, client relationship management, strategic thinking, and the wisdom to optimize for outcomes rather than just tax calculations. It’s where true tax professionals prove their worth by delivering advice that transforms clients’ financial lives.

Ready to master these strategic filing decisions that could save your clients thousands while protecting them from significant financial risks? Listen to Jeremy Wells walk through the complete framework for navigating married filing status elections, including real-world examples and technical details that will change how you approach these decisions.

Why S Corporation Elections Backfire More Often Than You Think

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Early in his accounting career, Jeremy Wells, EA, CPA, landed what seemed like the perfect client: a newly independent contractor drowning in tax debt to both the IRS and his state agency. Within just a couple of years, Wells helped transform this financial disaster into a success story. Through strategic S corporation planning, proper bookkeeping, and careful tax planning, his client went from owing thousands to receiving small but satisfying annual refunds.

The S corporation election was absolutely the right move. But Wells emphasizes that this was the right client at the right time, with the right circumstances.

In a recent episode of Tax in Action, “S-Corporation Reality Check,” Wells examines the oversimplified advice flooding social media feeds and startup marketing campaigns. While countless online voices promise S corporation elections deliver automatic self-employment tax savings for any successful self-employed person, Wells sees this advice creating expensive problems for businesses that never should have made the election in the first place.

“There’s a cottage industry developing around this concept,” Wells explains. We’re in a perfect storm where remote work and the gig economy have created lots of successful self-employed people who need tax help, but there’s a shortage of qualified advisors who can provide proper guidance.

The reality is, while this cottage industry promises easy self-employment tax savings, the one-size-fits-all approach ignores critical deal-breakers that can transform a supposed tax benefit into a costly mistake.

Balance Sheet Red Flags That Kill S Elections

The cottage industry’s relentless focus on self-employment tax savings completely sidesteps fundamental balance sheet realities that can make S elections counterproductive or even trigger unexpected taxable events.

The most dangerous misconception involves debt basis. Unlike partnerships, where partners receive basis credit for their share of entity debt, S corporation shareholders get no such benefit unless they personally loan money to the corporation.

“I can go get a loan and intend to use the funds in my S corporation, but if I personally guarantee that debt, that is not me generating debt basis,” Wells explains. “I am not loaning money to my corporation.”

This distinction catches many business owners—and their advisors—completely off guard. The COVID-era Economic Injury Disaster Loans are a perfect example of this misunderstanding. Thousands of sole proprietorships took personally-guaranteed SBA loans and later elected S corporation status, only to discover that their EIDL debt provided zero debt basis benefit. When these businesses generated losses, shareholders couldn’t deduct them against other income because they lacked sufficient basis.

But there’s another trap buried in the S election process itself. When an LLC elects S corporation status, the tax code requires a two-step transaction that most people don’t understand. First, the LLC becomes an association taxed as a C corporation, then immediately elects S status. During that first step, a Section 351 exchange occurs where the entity’s assets and liabilities transfer to the new corporation in exchange for stock.

Here’s where it gets dangerous: if the business has liabilities exceeding assets—not uncommon for debt-heavy service businesses with minimal fixed assets—this exchange creates taxable gain. “We might be inadvertently generating a taxable event for that owner or those partners when they make that selection,” Wells warns.

The equity structure challenges run even deeper. S corporations demand a single class of stock, pro-rata allocations of everything, and pro-rata distributions with no exceptions. “All items of income, loss, deduction, gain and credits must be allocated to the shareholders pro rata based on their percentages of ownership in the corporation stock, and there are no exceptions to that,” Wells notes.

This inflexibility is particularly problematic for businesses planning future acquisitions. Many small businesses today are built with acquisition in mind—not just Silicon Valley startups, but local businesses designed to be attractive to buyers within three to ten years. S corporations complicate these plans because many acquisition entities aren’t qualified S corporation shareholders. Non-US entities, partnerships, and C corporations can’t own S corporation stock, forcing expensive workarounds.

This is why Wells always asks clients about their long-term goals: “We always have to plan with the end in mind, especially when it comes to equity.”

Operating Agreements: The Hidden S Election Killers

The S corporation promotion industry systematically ignores a fundamental reality: most operating agreements are legal landmines for S elections. Wells’ firm learned this lesson the hard way, which is why they now require operating agreements from all multi-member LLC clients before making any S election recommendations.

“We read through it and try to pick out these terms and concepts and potential red flags,” Wells explains. What they consistently find are documents written exclusively for partnership taxation under Subchapter K—documents that can directly contradict the rigid requirements of Subchapter S.

The most dangerous provisions involve substantial economic effect requirements under Section 704(b). Partnership operating agreements routinely include liquidation provisions requiring distributions based on positive capital accounts. This creates non-pro-rata distribution requirements that are perfectly normal for partnerships but absolutely prohibited for S corporations.

Wells has encountered operating agreements that explicitly prohibit S elections, containing language like “this LLC will always be a partnership for tax purposes” or “the business cannot do any sort of corporate election.” Even more commonly, he’s seen agreements with waterfall distribution clauses that prioritize some members over others—a structure that violates S corporation pro-rata distribution requirements and can trigger inadvertent election termination.

Perhaps most problematic, Wells notes: “I have never seen an operating agreement in an original draft that listed out what happens if an S election takes place.” Most templates simply don’t consider the possibility, leaving businesses with agreements that actively work against their tax election goals.

Even operating agreements that appear silent on these issues often default to state partnership laws that can require non-pro-rata distributions. “If we have an operating agreement that doesn’t really cover these topics, that’s when state law intervenes,” Wells explains.

The solution requires proactive legal work that the quick-and-easy S corporation services don’t provide. Businesses need either revised operating agreements that explicitly allow for S elections or entirely new agreements written with tax flexibility in mind. This legal work might cost a few thousand dollars upfront, but it’s far cheaper than dealing with an inadvertent election termination that requires a private letter ruling or Tax Court intervention.

The Math Doesn’t Add Up: Hidden Costs and Incomplete Calculations

The S corporation promotion machine focuses entirely on self-employment tax savings while conveniently ignoring every other aspect of a client’s tax situation. This creates problems where businesses make expensive elections based on wildly inaccurate financial projections.

The most glaring flaw involves reasonable compensation requirements. “A lot of the estimates of tax savings with an S election just estimate reasonable compensation way too low,” Wells observes. “Those tax savings are not the result of the S election. Those tax savings are unreasonably low salaries being paid through those S corporations.”

It’s a mathematical sleight of hand. Of course, any advisor can eliminate 100% of self-employment tax by simply not running payroll to active S corporation shareholders. But this isn’t tax planning; it’s setting clients up for IRS problems down the road.

The Section 199A qualified business income deduction creates another calculation error that the cottage industry ignores. Higher reasonable compensation reduces the pass-through income that forms the basis for this valuable 20% deduction. As Wells explains: “We save a little bit of self-employment tax at the expense of a pretty significant deduction for a lot of small business owners.”

For many successful small business owners, losing substantial QBI deductions easily outweighs any self-employment tax savings from an S election.

State and local taxes deliver the knockout punch to many S election projections. Tennessee imposes a 6.5% tax on S corporations. New York City hits S corporations with an 8.85% rate. California charges the greater of $800 or 1.5% of net income. As Wells puts it, “Those taxes can wipe out any projected tax savings from an S election.”

A business owner in Tennessee could save $3,000 in federal self-employment tax only to pay $5,000 in additional state tax. The cottage industry’s federal-only analysis turns a supposed tax benefit into a $2,000 annual penalty.

The complications extend to asset transactions. S corporations create taxable gain when distributing appreciated property to shareholders, which is a problem that partnerships avoid. For businesses holding real estate or other appreciating assets, this difference can cost tens of thousands in unexpected taxes. That’s why Wells generally recommends not holding real estate in an S corporation.

Similarly, S corporations lose access to Section 754 elections that allow partnerships to step up the inside basis of assets when ownership changes. This valuable planning tool helps partnerships minimize taxes when partners sell their interests or inherit them. S corporations simply don’t have this option.

The Professional Alternative to Checkbox Solutions

The problems with S corporation election advice reveal a broader issue: complex tax decisions are being oversimplified into marketing soundbites. While the cottage industry profits from reducing professional judgment to self-employment tax calculators, tax professionals face a choice between participating in this race to the bottom or demonstrating why expertise matters.

“We need to seriously look at what that entity election will mean for the business today, in the future, and for the shareholders or partners themselves,” Wells says. This level of analysis requires understanding balance sheet implications, legal document conflicts, comprehensive tax calculations, and long-term business planning—expertise that can’t be packaged into a simple online service.

When clients arrive demanding an S election because “everyone online says it saves taxes,” the professional response isn’t to immediately comply or dismiss the idea. Instead, walk them through the complete analysis: balance sheet structure, operating agreement provisions, reasonable compensation realities, QBI impacts, state tax consequences, and future business goals.

This educational approach protects clients from expensive mistakes while positioning you as genuinely knowledgeable rather than just another order-taker. It creates long-term relationships built on trust and demonstrated expertise.

While the cottage industry promises simplicity, its oversimplified approach consistently creates far more complexity down the road. Inadvertent election terminations, operating agreement conflicts, unexpected state taxes, and acquisition complications all require costly professional intervention to resolve.

For tax professionals willing to master this complexity, the S corporation election presents both a professional responsibility and a market opportunity. Clients need advisors who can navigate the factors that determine whether an S election truly benefits their specific situation.

Good tax advice requires understanding the complete client situation, not just plugging numbers into a self-employment tax calculator. 

To hear Wells’ complete analysis and learn how to position yourself as the thoughtful alternative to the S corporation promotion industry, listen to the full Tax in Action podcast episode where he details the specific questions to ask and analyses to perform that separate professional advice from marketing-driven recommendations.

Why Two Identical 1031 Exchanges Had Opposite Outcomes in Tax Court

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Two real estate investors. Two 1031 exchanges. Two family members moving into replacement properties. One investor successfully deferred taxes, while the other faced a costly audit that wiped out their claimed benefits entirely.

The difference wasn’t timing, family relationships, or even rental income. It was something far more subtle: the ability to prove genuine investment intent through documented business behavior that could withstand IRS scrutiny.

In Click v. Commissioner, the taxpayer’s relatives moved into the replacement properties the day after the exchange closed. Seven months later, she gifted both properties to those families. The Tax Court saw through what it called a sham transaction.

But in Adams v. Commissioner, when the taxpayer’s son moved into the replacement property and paid below-market rent, the court sided with the taxpayer. The exchange qualified despite the family connection and reduced rental income.

In a recent episode of the Tax in Action podcast, host Jeremy Wells broke down the 1031 fundamentals to explain why the transaction worked out for one taxpayer and not another. While Section 1031 exchanges offer real estate investors a powerful tool to defer capital gains taxes, success depends on more than following the rules. It requires proving genuine business intent through careful documentation.

Understanding the 1031 Exchange Foundation

Here’s what Section 1031 does: it allows you to exchange property held for productive use in a trade, business, or investment for like-kind property with the same intended use. But there’s a crucial point many miss: Section 1031 defers gain; it doesn’t eliminate it.

Wells explains, “There is a misconception out there among taxpayers who could use or want to use section 1031 exchanges that 1031 just eliminates the gain from a like-kind exchange.”

When you exchange one property for another, you don’t avoid taxes; you postpone them. The deferred gain carries forward, and the replacement property takes the same basis as the original property. Eventually, when you sell the replacement property in a taxable transaction, you’ll pay tax on both the original deferred gain and any subsequent appreciation.

Since the Tax Cuts and Jobs Act took effect in 2018, 1031 exchanges only work for real estate. But within that category, the definition of “like kind” is remarkably broad. You can exchange an apartment building for raw land, a commercial office building for a single-family rental, or developed property for agricultural land.

The key requirement is that both properties must be held for productive use in trade, business, or investment. You can’t use a 1031 exchange for your personal residence or vacation home that you use strictly for personal purposes.

The Intent Test That Trips Up Investors

The biggest challenge with 1031 exchanges isn’t the technical requirements; it’s proving you genuinely intended to hold the replacement property for investment or business use. Wells points out that this has become “a question of facts and circumstances that has to be determined at the time of the exchange itself.”

The courts have seen numerous attempts by taxpayers to use 1031 exchanges to defer gain on what were essentially personal property acquisitions disguised as investments. This leads to intensive scrutiny of taxpayer motivation, regardless of whether they follow all the mechanical rules correctly.

Consider the Moore v. Commissioner case. The taxpayers exchanged one vacation property for another, using both properties personally without any rental activity. When audited, they argued they held the properties for “investment,” meaning they expected the properties to appreciate in value.

The Tax Court disagreed. “Just the mere expectation of an increase in value is not sufficient to establish that investment intent,” Wells notes. Simply hoping property values will rise doesn’t qualify as holding property for investment under Section 1031.

This reveals how enforcement has evolved. Technical compliance with timing rules and intermediary requirements won’t protect you if your behavior contradicts your stated investment intent. The IRS looks at the complete picture surrounding each exchange.

What the Court Cases Reveal About Documentation

The contrast between successful and failed exchanges often comes down to documentation quality, not transaction structure. Let’s examine what separated the winners from the losers.

The Click Failure

The taxpayer exchanged her farm for two residential properties. Her children moved into those houses the day after the exchange closed. Seven months later, she gifted both properties to the families. Her defense crumbled because she couldn’t demonstrate any genuine rental activity during those seven months. The court saw this as a sham transaction designed to defer gain on personal property transfers.

The Adams Success

This taxpayer exchanged a rental property for a fixer-upper. His son moved in and began extensive renovations, living there during a three-month repair period in exchange for renovation work. After that, the father began charging rent. Yes, the rent was below market rate, and the son missed one payment. But the court saw a consistent pattern of business-like behavior: formal rental arrangements, regular cash payments, and documented property improvements.

The Goolsbee Disaster

 These taxpayers placed a single advertisement in a neighborhood newsletter and moved into the replacement property within two months. When questioned during the audit, they couldn’t even answer whether rentals were allowed in their community. Their minimal marketing effort and inadequate preparation convinced the court that their investment intent was fabricated.

The Reesink Victory

Even though these taxpayers moved into their replacement property after eight months, they had a compelling record of genuine rental attempts: multiple flyers distributed around town, documented property showings to prospective tenants, and one potential renter who actually testified in court on their behalf.

Wells emphasizes the key insight: “It’s not necessarily a matter of waiting a certain number of months. It’s not a matter of whether you advertised that property for rent or not. It’s the culmination of all of these different facts and circumstances.”

The Technical Requirements You Must Follow

Beyond proving intent, you need to navigate specific compliance requirements that can make or break your exchange.

Timing Rules for Deferred Exchanges

Most 1031 exchanges today are deferred exchanges, where the sale and purchase don’t happen simultaneously. You have two critical deadlines:

  • 45-day identification rule. You must identify replacement property within 45 days after closing on the sale of your original property. This identification must be in writing, signed, and sent to someone involved in the exchange.
  • 180-day completion rule. You must receive the replacement property within 180 days of transferring the original property, or by the due date (including extensions) of your tax return for that year, whichever comes first.

Safe Harbor Requirements

The most common approach uses a qualified intermediary who holds the proceeds from your property sale and facilitates the replacement property purchase. The key is that you never have control of the funds from the original property sale.

Disqualified Persons

You can’t do exchanges with certain people, including your employees, attorneys, accountants, investment brokers, bankers, or real estate agents, if they’ve worked for you within the past two years. You also can’t exchange with close family members or entities where you own more than 10% of the stock or partnership interest.

Geographic Restrictions

You cannot exchange U.S. real estate for foreign real estate, or vice versa. Wells notes he’s “had to advise clients on this before because they want to start dabbling in rental markets outside the U.S.” or dispose of foreign properties to build their U.S. portfolio.

Reporting and Ongoing Obligations

Taxpayers must report successful 1031 exchanges on Form 8824, which has three main parts: property descriptions with key dates, related party disclosures (if applicable), and calculation of deferred gain and basis in the replacement property.

If your exchange involves related parties, you must file Form 8824 for two years after the exchange, and neither party can sell their received property during that two-year period without potentially disqualifying the exchange.

The replacement property continues the depreciation schedule from the original property. “Wherever we’re at in the depreciable life, the number of years of depreciation, the accumulated depreciation of the relinquished asset, we’re going to carry that over generally into the new asset,” Wells explains.

Building Your Defense Strategy

Enforcement of 1031 exchange rules has fundamentally shifted from checking compliance boxes to evaluating business narratives. Every marketing effort, tenant interaction, and business decision becomes part of a story that auditors may scrutinize for evidence of authentic business purpose.

When helping clients with 1031 exchanges, focus on creating documentation that demonstrates genuine investment intent:

  • Document all rental marketing efforts thoroughly
  • Maintain records of tenant interactions and property showings
  • Keep evidence of rental income and expenses
  • Avoid personal use that could undermine investment intent
  • Create a paper trail that supports your business purpose

A failed 1031 exchange can trigger penalties and interest that devastate investment returns. But when properly structured and documented, these exchanges provide real estate investors with a powerful tool for building wealth through tax-efficient property portfolios.

Wells’ comprehensive exploration provides the technical foundation every practitioner needs, but your ability to tell a compelling business story through consistent, credible evidence often matters more than perfect technical compliance.

For the complete technical framework and additional insights that can help you guide real estate investor clients through successful exchanges, listen to Wells’ full Tax in Action episode.