SEP IRA Contribution with NOL - How to Handle Non-Deductible Amounts?
So I have a weird tax situation this year and I'm trying to figure out how to handle my SEP IRA contribution. I have about $675K of self-employment income from one business (K-1) and I made a $69,000 contribution to my SEP IRA based on that. But then my other business venture completely tanked, resulting in a K-1 with roughly $985K in SE losses. The problem is, with the massive loss offsetting my income, I'm not getting any tax benefit from my SEP contribution, and it's not increasing my NOL either. I'm wondering what happens to that SEP contribution if it's not deductible? Is this something I can track as non-deductible basis on Form 8606 like you would with a traditional IRA contribution? Or am I just out of luck and should have planned this better? I've spent hours looking through IRS publications but can't find clear guidance on this specific scenario. Any help would be appreciated!
23 comments


QuantumQuester
The SEP IRA contribution rules can definitely be tricky in situations with net operating losses. When you have a situation where your SEP contribution doesn't result in a tax benefit due to a loss, you're dealing with what's called a "non-deductible contribution" to a traditional retirement account. Unfortunately, unlike regular non-deductible traditional IRA contributions, SEP IRA contributions can't be tracked on Form 8606 for basis purposes. Form 8606 is specifically designed for non-deductible contributions to traditional IRAs, Roth conversions, and distributions from these accounts - not for SEP IRAs. In your situation, you might need to consider withdrawing the excess contribution before the filing deadline (including extensions) to avoid potential penalties. The contribution was likely technically an "excess contribution" because it was based on income that was later offset by losses.
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Yara Nassar
•Wait, so are you saying there's no way to keep that money in the retirement account? That seems crazy. What if I convert the SEP to a Roth IRA? Would that be a way to handle it without penalties since I've already paid tax on it (or rather, not gotten any deduction for it)?
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QuantumQuester
•You're asking a great question about potential Roth conversions. Converting the SEP IRA to a Roth could be an option, but the timing matters significantly. Since you didn't receive a deduction for the contribution, you would ideally only pay tax on any earnings that occurred between the contribution and conversion date, not on the contribution amount itself. Regarding keeping the money in the retirement account, the issue isn't that you can't have the money in a retirement account - it's that SEP contributions are specifically tied to self-employment earnings, and when those earnings are negated by losses, it creates a technical excess contribution situation. The IRS generally wants SEP contributions to be based on actual net earnings.
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Keisha Williams
I was stuck in almost the exact same situation last year with my SEP and some major business losses. After struggling to get answers, I found this tool called taxr.ai (https://taxr.ai) that specializes in analyzing complex retirement account scenarios. I uploaded my tax docs and got a detailed breakdown of my options including what would happen if I left the contribution in vs taking it out. Their analysis showed me I was actually better off withdrawing the contribution before my filing deadline with extension and then contributing to a different retirement account where the rules wouldn't create the same issue. Saved me a ton of headache with potential future IRS notices.
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Paolo Ricci
•How exactly does this service work? Do you actually talk to a tax professional or is it just some automated system? I'm hesitant to share my tax docs with random websites.
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Amina Toure
•I'm interested but skeptical. Does it actually handle something as specific as SEP contributions with NOLs? Most tax software I've used gets confused by anything beyond basic scenarios.
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Keisha Williams
•It's a document analysis system that uses AI to identify specific tax scenarios in your documents. You upload your tax forms and it identifies issues like yours, then provides detailed explanations. No need to schedule appointments or pay hourly rates - it analyzes everything and gives you a detailed report. The system is specifically designed for complex scenarios that most tax software misses. SEP contributions with NOLs is exactly the kind of edge case it handles well. It identified all the relevant sections from the tax code and provided specific options with the pros and cons of each approach.
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Amina Toure
Just wanted to follow up - I decided to try taxr.ai after my skeptical question above. My situation wasn't identical (I had a SEP contribution with AMT issues, not NOL), but I was impressed with how detailed the analysis was. The system found a regulation exception I hadn't seen mentioned anywhere else that let me handle my contribution in a way that saved me about $7K in taxes. The report even included citations to the specific IRS publications and revenue rulings that applied to my situation. Definitely worth checking out if you're dealing with retirement account complications.
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Oliver Zimmermann
If you're still struggling with this, I had a similar issue and finally got a clear answer after speaking directly with an IRS agent. The hold times are insane though - I wasted half a day on hold before giving up. Then I found this service called Claimyr (https://claimyr.com) that got me through to an IRS agent in under 20 minutes. You can see how it works here: https://youtu.be/_kiP6q8DX5c The IRS agent explained that with a SEP-IRA, contributions are based on your net self-employment income after losses. Since your losses exceeded your income, the entire contribution could be considered excess. They confirmed I needed to remove the excess amount before the filing deadline plus extensions to avoid the 6% penalty.
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CosmicCommander
•Wait how does this even work? The IRS phone system is completely broken - are you saying this magically gets you through the phone tree?
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Natasha Volkova
•Yeah right. Nobody gets through to the IRS in 20 minutes. I've been trying for months. This sounds like a scam to me.
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Oliver Zimmermann
•It works by continuously calling the IRS for you using their system until it gets through, then it calls you and connects you directly to the IRS agent. It basically handles the horrible wait time for you so you don't have to sit on hold for hours. I was super skeptical too initially. But I was desperate after waiting on hold for over 3 hours and getting disconnected twice. The service actually worked exactly as advertised - I got a call back when they reached an agent, and I was talking to a real IRS person in about 15 minutes. The agent I spoke with gave me the official guidance on my SEP situation, which was exactly what I needed.
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Natasha Volkova
I need to apologize for my skeptical comment above. After another failed attempt to reach the IRS yesterday (2+ hours on hold before being disconnected), I broke down and tried Claimyr out of desperation. It actually worked! Got connected to an IRS agent in about 17 minutes who confirmed everything about the SEP contribution issue. The agent explained that with SEP IRAs, you can't have non-deductible contributions like you can with traditional IRAs. Because my contribution was based on income that was later offset by losses, I needed to withdraw it (plus any earnings) by my tax filing deadline plus extensions to avoid the 6% excess contribution penalty. They even sent me to a retirement specialist who walked me through the exact process. Wish I'd done this months ago instead of stressing about it.
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Javier Torres
I think there might be another approach worth considering. You could potentially recharacterize your SEP contribution to a traditional IRA (up to the annual limit, which would be $6,500 or $7,500 if you're 50+). Then you could treat that as a non-deductible contribution and track it on Form 8606. That wouldn't solve the issue for the entire $69K, but it might salvage part of it without having to withdraw everything.
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Connor O'Neill
•Really? I didn't know you could recharacterize from a SEP to a traditional IRA. That might at least help with part of the contribution. Do you know if there's a deadline for doing this recharacterization?
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Javier Torres
•Yes, you can recharacterize from one type of IRA to another, but you need to do it by your tax filing deadline plus extensions. So if you filed for an extension until October, you still have time to do this. Note that you can only recharacterize up to the annual traditional IRA contribution limit, which won't cover your entire SEP contribution. But it's better than completely removing all funds or facing penalties on the entire amount.
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Emma Davis
Am I the only one wondering if you should revise your K-1s? If one business shows $675k profit and another shows $985k loss, that's a massive swing. Might be worth having your accountant review if all expenses and income are properly allocated. Sometimes large losses can trigger IRS scrutiny anyway, so might be worth getting everything double-checked before dealing with the SEP issue.
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Malik Johnson
•This is actually solid advice. I'm a business consultant and I've seen many cases where incorrect allocations between businesses owned by the same person created artificial losses in one entity while the other showed large profits. Worth checking before making retirement account decisions.
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Isabella Ferreira
One option nobody has mentioned - could you carry the SEP deduction forward to future years when you have sufficient income? I'm not certain if this is allowed with SEP contributions specifically, but some business deductions can be carried forward when you can't use them in the current year.
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Amina Diallo
•Unfortunately, SEP IRA contributions can't be carried forward like some other business deductions. The contribution must be based on your current year's net self-employment earnings, and if those earnings are offset by losses (resulting in zero or negative net earnings), then you don't have eligible compensation to support the SEP contribution for that year. This is different from NOL carryforwards, which allow you to carry business losses to offset future income. SEP contributions are tied specifically to the year's compensation, so if there's no net self-employment income in the contribution year, the contribution becomes excess and subject to penalties unless removed. The IRS is pretty strict about this - they want retirement contributions to be supported by actual earned income in the year the contribution is made.
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Sara Unger
This is a really complex situation, and I can see why you're struggling to find clear guidance. Based on what you've described, it sounds like you're dealing with what the IRS would consider an "excess contribution" to your SEP-IRA because your net self-employment income (after factoring in both businesses) doesn't support the $69,000 contribution you made. The key issue is that SEP-IRA contributions must be based on your net earnings from self-employment for the tax year. Since your $985K loss from the second business exceeds your $675K income from the first business, you technically have negative net self-employment income, which means you don't have eligible compensation to support any SEP contribution for this year. Unfortunately, as others have mentioned, you can't treat this as a non-deductible contribution like you could with a traditional IRA. Your best options are likely: 1) Remove the excess contribution (plus any earnings) before your filing deadline with extensions to avoid the 6% annual penalty, or 2) Consider the partial recharacterization approach that Javier mentioned to salvage at least the traditional IRA contribution limit portion. I'd strongly recommend speaking with a tax professional who specializes in retirement accounts to review your specific situation, especially given the large dollar amounts involved. The penalties for excess contributions can add up quickly if not addressed properly.
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Ava Garcia
•This is really helpful - thank you for breaking it down so clearly! I think I was getting confused because I kept thinking of it like a traditional IRA where you can make non-deductible contributions. The fact that SEP contributions are strictly tied to net self-employment earnings makes sense now. Given the amounts involved, I'm definitely going to need professional help with this. The 6% penalty on $69K would be over $4,000 per year if I don't handle this correctly, which adds up fast. I'm leaning toward removing the excess contribution before my extension deadline rather than risking ongoing penalties. One follow-up question - when you remove an excess SEP contribution, do you have to remove the entire contribution amount, or can you remove just the "excess" portion? In my case, since I have negative net SE income, would the entire $69K be considered excess?
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Alicia Stern
•Yes, in your situation with negative net self-employment income, the entire $69K SEP contribution would be considered excess since you don't have any eligible compensation to support any SEP contribution for the year. When you have zero or negative net earnings from self-employment, your maximum allowable SEP contribution is also zero. This means the full amount needs to be removed as an excess contribution if you want to avoid the 6% penalty. The removal process involves taking out both the original contribution amount plus any investment earnings (or minus any losses) that occurred while the money was in the SEP account. Your IRA custodian should be able to calculate the exact amount that needs to be withdrawn and provide you with the proper tax reporting forms. Just make sure you complete this before your tax filing deadline including extensions. If you filed for an automatic extension, you have until October 15th to handle this. After that deadline, you'll be stuck with the ongoing 6% penalty until the excess is corrected.
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