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Amara Adeyemi

S Corp SEP IRA Contribution Rules - Questions About Eligibility with Losses

Hey everyone, I've got some questions about SEP IRA rules with my S Corp side business. I'm the only employee and pay myself through a regular W-2 from Gusto. From what I've researched, my S Corp can contribute 25 percent of my W-2 wages (W-2 line 1 x .25) and write it off as a business expense. But I'm confused about a few things: 1) My S Corp is running at a loss this year, but I have positive retained earnings from previous years. Can I still make a SEP IRA contribution despite the current year loss? 2) For my W-2 paperwork, should I tell my payroll company about the SEP IRA contribution so they can check off the retirement plan box in Box 13? Or is that box only for employee contributions? Right now, only my S Corp entity will be contributing. 3) On contribution limits - just double-checking my math here. If my W-2 salary shows $13,500 on line 1, can my S Corp contribute $3,375 to the SEP IRA? I know the maximum allowed is $61,000 for 2022. 4) If I decide to switch to a Solo 401k next year instead, will having this SEP IRA mess up my eligibility? 5) I'm assuming the K-1 pass-through income doesn't factor into calculating my SEP IRA contribution limit for the S Corp, right? Thanks for any help you can provide! This tax stuff makes my head spin.

Yes, you can still make SEP IRA contributions even if your S Corp has a current year loss, provided you have W-2 wages from the business. The contribution is based on your compensation, not the profitability of the business. Your positive retained earnings from previous years aren't directly relevant to this calculation. For your W-2 question, yes, the retirement plan box in Box 13 should be checked if you're covered by a SEP IRA plan, even if only the employer is contributing. Let your payroll provider know so they can mark this correctly, as it affects your eligibility for deducting traditional IRA contributions. Your understanding of the contribution limit is correct. If your W-2 salary is $13,500, your S Corp can contribute up to $3,375 (25% of your W-2 wages). The overall limit of $61,000 for 2022 won't come into play at your current compensation level. Setting up a SEP IRA this year won't jeopardize your eligibility for a Solo 401(k) next year. You can establish a Solo 401(k) and stop making SEP contributions, though you'll need to keep the existing SEP IRA account. And you're absolutely right that K-1 pass-through income is not considered when calculating SEP IRA contributions for an S Corp. Only your W-2 wages count for this purpose.

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Thanks for your explanation, but I'm still confused about the loss situation. If the S Corp can't afford to make the contribution because it's already losing money, wouldn't that be an issue? Also, does the IRS look at this suspiciously if you're contributing to retirement while the business is in the red?

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From a tax perspective, you can absolutely make the contribution even with a loss. The SEP contribution is simply another business expense, like salary. The IRS isn't concerned about profitability when determining contribution eligibility - only that you have eligible compensation (your W-2 wages). The practical question of whether the business has enough cash to make the contribution is separate from tax eligibility. If you have the cash available in your business account (perhaps from operations in previous years), you can make the contribution despite showing a current year loss. This won't raise any red flags with the IRS as it's a legitimate business expense based on compensation paid.

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Dylan Wright

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I've been navigating S Corp retirement plans for years and finally found a solution that cut through all the confusion. I was in a similar situation trying to understand SEP IRA contributions with my S Corp showing losses in some years. After spending hours on IRS publications and getting conflicting advice, I tried https://taxr.ai and it was a game changer. Their system analyzed my S Corp structure, previous tax returns, and clarified exactly what I could contribute despite my losses. It specifically addressed how W-2 wages are the determining factor for SEP IRAs regardless of business profitability. They even provided documentation I could share with my accountant to back up their analysis. What I appreciated most was how they explained the Box 13 retirement plan checkbox implications - something none of my other advisors clearly addressed.

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NebulaKnight

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I'm intrigued but skeptical. Does it actually connect you with a tax professional or is it just analyzing documents? My situation is similar but I also have a regular job with a 401k and I'm wondering if that would complicate things.

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Sofia Ramirez

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How quickly did you get answers? I need this info like yesterday because I'm trying to decide between SEP and Solo 401k before year-end and my accountant is on vacation until next week.

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Dylan Wright

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It's primarily document analysis - you upload your tax returns and corporate docs, and their AI system analyzes everything and creates a comprehensive report. There's also an option to get clarification from their tax team if something isn't clear. For your situation with an outside 401k, that's exactly the type of complexity their system handles well - it would show you how both plans interact and your total contribution limits. The turnaround time is surprisingly fast - I got my initial analysis in about 2 hours. It's specifically designed for these time-sensitive decisions between retirement plan options. It broke down the differences between SEP IRA and Solo 401k based on my specific numbers, which made my decision much clearer than the general advice I was finding elsewhere.

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Sofia Ramirez

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Just wanted to follow up - I tried https://taxr.ai last week after seeing it mentioned here. It was actually really helpful for my situation. I was struggling with the same SEP IRA questions with my S Corp that's currently running at a loss. The report clearly showed that I could still make my SEP contribution based on my W-2 wages despite the loss, and explained exactly how to document it. It even created a calculation sheet showing exactly how much I could contribute based on my specific compensation. What really helped was their breakdown of SEP IRA vs Solo 401k with my exact numbers. Based on their analysis, I'm switching to Solo 401k next year since I'll be able to contribute significantly more with the same W-2 salary. They explained that the Solo 401k allows employee deferrals of up to $20,500 PLUS the employer contribution, while the SEP only allows the employer portion. Definitely worth checking out if you're dealing with S Corp retirement plan questions.

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Dmitry Popov

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I had the exact same questions last year! After spending HOURS trying to reach the IRS for clarification (seriously, I spent over 2 weeks calling), I finally found https://claimyr.com and their service to get through to an actual IRS agent. You can see how it works here: https://youtu.be/_kiP6q8DX5c The IRS agent confirmed that yes, you can contribute to a SEP IRA with W-2 wages even when your S-Corp has losses. They explained that the contribution is based on compensation, not profit. They also clarified that Box 13 should definitely be checked since it indicates plan coverage, not contribution source. The conversation saved me thousands in potential penalties because I was about to skip the SEP contribution entirely, thinking it wasn't allowed during a loss year. Now I make sure all my S Corp clients understand these rules.

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Ava Rodriguez

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How does this Claimyr thing actually work? I've been trying to reach the IRS for weeks about a similar issue. Do they just keep calling for you or something?

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Miguel Ortiz

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Yeah right. Nobody gets through to the IRS these days. I've tried calling at least 20 times this month and either get disconnected or told the wait time is over 2 hours. I'll believe this works when pigs fly.

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Dmitry Popov

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It uses a system that continuously dials the IRS until it gets through their busy signals and holds your place in line. When they reach a human agent, you get a call connecting you directly to that agent. It basically does the waiting for you so you don't have to sit on hold for hours. I was extremely skeptical too before trying it. I had spent literally weeks trying to get through on my own with no luck. But I was desperate for answers about my S Corp retirement options before the filing deadline. The service got me through to an IRS representative in about 3 hours (while I was working on other things). The agent gave me clear confirmation about SEP IRA contributions during loss years and answered all my other questions. Honestly, the clarity was worth every penny after all the conflicting advice I was getting.

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Miguel Ortiz

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I have to admit I was completely wrong about Claimyr. After posting that skeptical comment, I was desperate enough to try it because I needed clarification on a similar S Corp retirement plan issue before making my year-end contributions. The service actually worked! I got connected to an IRS agent the same day after trying unsuccessfully for weeks on my own. The agent confirmed everything about SEP IRAs with S Corps - yes you can contribute with a business loss as long as you have W-2 wages, and the Box 13 should be checked even if only the business is contributing. I even asked about switching to a Solo 401k next year and got confirmation that it wouldn't be a problem. The agent explained that I'd need to establish the Solo 401k by December 31st if I want to use it next year, something none of the online articles mentioned. Definitely worth the call!

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Zainab Khalil

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One thing nobody's mentioned yet that I think is important - if you're thinking about switching to Solo 401k next year, you should know there are administrative differences. SEP IRAs are super simple with almost no paperwork, but Solo 401ks require a plan document and potentially Form 5500-EZ filing if your plan assets exceed $250k. That said, I've used both with my S Corp and still prefer the Solo 401k because of the higher contribution limits. With a SEP, you're capped at 25% of W-2 wages from the employer side only. With Solo 401k, you can do the same 25% employer contribution PLUS contribute up to $20,500 (2022 limit) as an employee deferral, even if that takes you above the 25% limit.

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QuantumQuest

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Do you use a specific provider for your Solo 401k? I've heard some have much better options than others, especially for someone who might want to do a Roth option or take a loan from the plan eventually.

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Zainab Khalil

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I use Fidelity for my Solo 401k. They offer both traditional and Roth options for the employee contribution portion, which is a huge advantage. Their plan doesn't allow loans, but that wasn't important for my situation. If loans are important to you, check out E*TRADE or TD Ameritrade. The paperwork was surprisingly minimal - just a one-time plan adoption agreement. I haven't had to file Form 5500-EZ yet since my balance is still under $250k. The investment options are excellent and there are no setup or maintenance fees, which was important to me.

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Connor Murphy

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Just want to add about the Box 13 checkbox - it's super important for your overall tax situation! If that box isn't checked and you're actually covered by a retirement plan, you could accidentally claim deductions for traditional IRA contributions when you're not eligible. That can result in penalties later if the IRS catches it. I learned this the hard way a few years ago when my S Corp made SEP contributions but my accountant didn't communicate it to my payroll provider. The box wasn't checked, I contributed to a traditional IRA and took the deduction, and ended up having to file an amended return and pay penalties.

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Amara Adeyemi

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That's exactly the kind of situation I want to avoid! So even though the S Corp is making the contribution and not me personally, the Box 13 still affects my personal IRA deductions? That seems really counterintuitive.

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Yes, that's exactly right! Even though your S Corp is making the SEP contribution (not you personally), you're still considered "covered" by a retirement plan for IRS purposes. The Box 13 checkbox indicates plan coverage, which then affects your ability to deduct traditional IRA contributions based on your income level. If you're covered by a workplace retirement plan (including SEP IRAs), your traditional IRA deduction phases out at lower income levels. For 2022, if you're single and covered by a plan, the deduction starts phasing out at $68,000 of modified AGI. Without the Box 13 checked, the IRS systems won't flag this limitation. It's one of those interconnected tax rules that isn't obvious - your business retirement plan affects your personal tax planning. Definitely make sure your payroll provider understands this!

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Ethan Brown

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This is such a helpful discussion! I'm in a similar boat with my S Corp and was getting confused by all the different rules. One thing I'd add that helped me understand the loss situation better - think of the SEP contribution as just another payroll expense, like your regular salary. The fact that your business shows a loss doesn't prevent you from paying yourself wages, and it doesn't prevent you from making retirement contributions based on those wages either. The loss might actually be partially due to the salary and SEP contribution expenses themselves! For what it's worth, I've been making SEP contributions for three years now, including one year where my S Corp had a small loss, and never had any issues with the IRS. The key is just making sure you have the cash flow to support it and that your contribution doesn't exceed 25% of your W-2 wages. Your math on the $13,500 salary and $3,375 contribution looks spot on. Just make sure to coordinate with your payroll company about that Box 13 - it really does matter for your personal tax situation down the road.

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Mei Wong

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This really helps clarify things! I've been overthinking the loss situation. You're absolutely right that the SEP contribution is just another business expense like payroll. I'm curious though - when you had that year with a small loss, did you still get the full business deduction for the SEP contribution? I assume it just increased your loss for the year, which then flowed through to your personal return as an ordinary loss. Is that how it worked? Also, thanks for confirming the math. I was second-guessing myself on the 25% calculation but it sounds like I've got it right. Now I just need to make sure I communicate clearly with my payroll company about checking that Box 13!

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