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How to withdraw funds from an S-Corp with minimal tax impact as minority shareholder?

I'm in a family S-Corporation with my brother where we're doing pretty well financially. I hold 2% ownership while he holds 98%. We both get K-1s showing our portion of profits that go on our personal tax returns. We both take regular salaries, but we also do occasional distributions. Last year I took out a fairly large distribution. Here's what I'm trying to understand: If our company makes $120K in profits after all expenses in 2024, he gets a K-1 for $117,600, I get one for $2,400. We pay taxes individually on those amounts, and technically the retained earnings can be withdrawn tax-free. But that creates an issue because if I withdraw more than my 2% share, he's essentially paying taxes on money I'm taking out! What I'd like to do is take a distribution of something like $15K and have that count as an expense BEFORE the K-1s are calculated. So company makes $120K - $15K = $105K, brother gets a K-1 for $102,900, I get one for $2,100, plus I have this $15K that I need to figure out the tax situation for. I haven't contributed additional capital to the business, only received various profit distributions, usually exceeding what's on my K-1. Previously I've treated these as bonuses, but they're actually profit distributions. How can I get that $15K into my personal account with minimal tax exposure? We haven't finalized our 2024 company return yet, so if there's a more advantageous (but completely legal and ethical) way to account for this, I'd love to know. I've read something about distributions being taxed at long-term capital gains rates if they exceed the shareholder's stock basis. Could this apply here? I honestly don't know what my stock basis is or how to calculate it. I paid very little for my 2% back in 2010. How do these distributions affect my stock basis? If my basis was hypothetically $6K, and I took $15K last year, would my basis now be negative ($9K)? What's the relationship between stock basis and ownership percentage? Should we have been tracking stock basis for each of us and adjusting ownership percentages yearly? Is the stock basis amount on the K-1, or is it a separate equity account I should have been tracking that none of our accountants ever mentioned? I've reached out to our accountant but thought I'd see what others know. What's the relationship between stock basis, ownership percentage, K-1 amounts, and shareholder distributions in S-Corporation taxation? How do these elements affect each other? And most importantly, how do I withdraw money from an S-Corp where I'm a 2% shareholder, in amounts significantly higher than what's on my K-1? Thanks to anyone who made it through all that!

I've been following this discussion with great interest as I'm in a very similar situation with our family S-Corp. The advice about increasing salary to market rates really resonates - I think many family businesses struggle with this because they focus so much on minimizing payroll taxes that they don't consider how proper compensation can actually solve distribution issues. One additional angle I'd suggest exploring: look into whether your S-Corp election is even still the best structure for your situation. With such unequal ownership but more equal contribution, you might benefit from converting to a partnership (LLC with partnership taxation) where you can have much more flexibility in profit allocations through the operating agreement. Partnerships allow for "special allocations" that can distribute profits based on contribution rather than ownership percentage, as long as they have substantial economic effect. This could eliminate the whole basis/gift tax issue you're dealing with. Obviously this is a major decision that would require professional guidance, but it's worth exploring whether the S-Corp structure is still serving your needs. Sometimes we get so focused on working within existing constraints that we don't step back and ask if those constraints are necessary. The conversion process has tax implications, but given the ongoing complexity you're facing, it might be worth running the numbers to see if a different entity structure would better match your economic arrangement.

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Avery Davis

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That's a really interesting perspective about potentially switching entity structures! I hadn't considered that the S-Corp election itself might be part of the problem rather than something we need to work around. The partnership allocation flexibility you mentioned sounds like it could solve a lot of these headaches, especially for family businesses where ownership percentages don't necessarily reflect current contributions. Do you happen to know if there are any significant costs or complications with converting from S-Corp to LLC status? I'm particularly curious about whether there would be any immediate tax consequences from the conversion itself. Also, @Gabriel Freeman, when you mention "substantial economic effect" for special allocations - is that something that's relatively straightforward to structure, or does it require really complex operating agreement language? I'm trying to weigh whether this would just trade one set of complications for another. The more I think about it, the more I realize we might have outgrown our original S-Corp structure as the business and our roles have evolved. Thanks for bringing up this bigger-picture perspective!

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Keisha Brown

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As someone who went through a very similar situation with our family S-Corp, I want to emphasize something that hasn't been mentioned enough: the importance of getting this straightened out BEFORE you file your 2024 return. The good news is you still have time to make salary adjustments for 2024 that could significantly help your situation. Since you mentioned you haven't finalized your company return yet, consider this approach: 1) **Immediate salary adjustment**: Calculate what reasonable market compensation should be for your actual role and responsibilities in 2024. If you can justify a higher salary based on work performed, you can still process additional payroll for 2024 (with proper payroll taxes) before year-end filing. 2) **Start tracking basis NOW**: Even if you have to estimate your historical basis, start with what you know and track going forward. Your 2024 K-1 will increase your basis, and any distributions reduce it. 3) **Document everything**: Whatever approach you take, make sure you have solid documentation for your reasoning. The IRS loves family S-Corps because they're often handled casually, but proper documentation protects you. The reality is that taking $15K in distributions on a $2,400 K-1 allocation puts you in capital gains territory once your basis is exceeded. But if you can restructure some of that as salary (assuming you can justify the work performed), you solve the problem at the source. Don't try to get too creative with the accounting - stick to legitimate business purposes and reasonable compensation standards. Your accountant should be able to help you model different scenarios before you file.

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This is excellent advice about timing! I'm actually in a very similar boat - just discovered I've been handling S-Corp distributions incorrectly for the past few years and my accountant never flagged the basis issues. The point about making salary adjustments before filing is crucial. I just realized I could potentially reclassify some of my 2024 "distributions" as additional salary if I can document the work I actually performed. Even though it means paying payroll taxes, it's probably better than the capital gains hit plus the complications with my business partner. @Keisha Brown, when you mention processing additional payroll for 2024 before filing - is there a specific deadline for this? I want to make sure I don't miss the window to make these adjustments retroactively. Also, for anyone else following this thread, I found that documenting actual hours worked and comparing to industry salary surveys really helped justify the compensation adjustments to our CPA. It's not just about wanting more money - it's about properly reflecting the economic reality of the work being performed. Thanks for all the practical guidance in this thread - it's been incredibly helpful for those of us trying to clean up these family S-Corp situations!

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Can someone explain how the 6% penalty actually works? If OP contributed like $3000 to their HSA without being eligible, is the penalty just 6% of that amount ($180)? Might be easier to just pay that than go through all the hassle of corrective distributions especially if they already used the money.

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Demi Lagos

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That's pretty much right - it's 6% of the excess amount for each year the excess remains in the account. So if they contributed $3000 without being eligible, they'd owe $180 for 2024. But if they don't remove it, they'd owe another $180 for 2025, and so on.

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Teresa Boyd

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I went through this exact situation two years ago and it's definitely stressful! A few things to keep in mind that might help: First, time is critical - you have until your tax filing deadline (including extensions) to remove the excess contributions and avoid the penalty entirely. Since you mentioned you're filing now, you still have time if you act quickly. Second, even though you spent the HSA money, you can still do a corrective distribution. You'll need to deposit funds back into the HSA first (equal to your excess contributions), then immediately request the corrective distribution from your HSA administrator. Yes, it's a bit of a hassle, but it's way better than paying 6% annually. Your HSA administrator should be able to help with the paperwork - most have dealt with this before. They'll need to calculate any earnings on the excess contributions too, which also need to be withdrawn. The key thing to remember is that using the money for qualified medical expenses doesn't fix the eligibility issue. The IRS is strict about who can contribute to HSAs, but they do give you options to correct mistakes if you act within the deadline. Don't panic - this is fixable! Just contact your HSA administrator ASAP to start the corrective distribution process.

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This is really helpful advice! I'm in a similar boat and have been putting off dealing with this because it seemed so complicated. One quick question - when you say "deposit funds back into the HSA first" - does this count as a new contribution that could also be subject to penalties if you're still not HSA-eligible? Or is it treated differently since it's just to facilitate the corrective distribution?

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Dylan Wright

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I'm in a very similar situation - filed on March 5th, accepted March 6th, and now it's been over two weeks with just "Your tax return is being processed" showing up. I also claimed EITC this year which I hadn't in previous years, so that's definitely adding to the processing time. What's been helpful for me is setting up IRS account online so I can access my tax transcripts. Even though the transcript codes are confusing, at least I can see that my return is in the system and there's some activity happening behind the scenes. The "Where's My Refund" tool is pretty basic and doesn't show the full picture of what's going on. I've also learned from this thread that checking daily doesn't help since it only updates weekly. I'm trying to be patient and give it the full 21+ days that seems to be normal for returns with credits this year. The waiting is definitely stressful when you're counting on that money though - I totally get that feeling!

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Miguel Ortiz

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That's a great tip about setting up the IRS account to view transcripts! I hadn't thought of doing that. Even if the codes are confusing, it would be reassuring to at least see that there's some movement happening behind the scenes rather than just staring at that vague "processing" message. I'm also trying to break the daily checking habit - it's become almost compulsive at this point! Maybe I should set a specific day of the week to check instead of randomly throughout the day when I'm feeling anxious about it. The 21+ day timeline definitely helps set realistic expectations, especially knowing that EITC adds extra verification time. Thanks for sharing your experience!

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I'm dealing with the exact same frustrating situation! Filed on March 1st, accepted March 3rd, and it's been 3 weeks of that same "Your tax return is being processed" message with absolutely no progress indicators. I also claimed EITC this year since my income qualified me for it for the first time. Reading through all these comments has been really helpful though - I had no idea that EITC claims automatically add extra processing time for verification. That explains why my coworker who filed the same day already got her refund last week while I'm still waiting. The daily checking obsession is so real! I've probably refreshed that "Where's My Refund" page 50+ times even knowing it only updates weekly. I'm going to try limiting myself to checking just on Sundays from now on to preserve my sanity. It's reassuring to know that 21-25 days seems to be the normal timeframe this year for returns with credits, even though it feels like forever when you're counting on that money. I was starting to worry something was wrong with my return, but sounds like this is just the reality of claiming refundable credits during peak season. Thanks everyone for sharing your experiences - makes the wait feel less scary!

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I'm going through the exact same thing! Filed March 4th, accepted March 5th, and I'm also stuck in that "processing" limbo for almost 3 weeks now. Also claimed EITC for the first time since I changed jobs and my income dropped enough to qualify. The daily checking habit is so hard to break - I've been obsessively refreshing that tool multiple times a day even though I know logically it won't change until the weekly update. Setting a specific day to check is a great idea, I think I'll try that too! What's been driving me crazy is seeing people on social media who filed after me already posting about getting their refunds. But now I understand it's because they probably didn't claim any credits that require extra verification. The 21-25 day timeline with EITC makes total sense when you think about how many returns they have to manually review during peak season. Thanks for sharing - it really does help to know we're all in the same boat waiting for those extra verification steps to complete. Fingers crossed we'll all see movement soon!

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NebulaNinja

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I just went through this exact situation last month! The IRS will definitely send your verification letter to the address on your 2023 tax return (the one you filed February 3rd), not what's currently showing on their website. Their online portal can take 4-6 weeks to update after processing, so don't worry about the address mismatch you're seeing there. Since you filed over two months ago, your return should be fully processed and the letter will go to your filing address. I waited about 8 days for mine to arrive. If you need faster access, you could try the ID.me verification route through their website - it's instant and bypasses the mail entirely. Just make sure someone can check the mailbox at your filing address if you're not there regularly. The letter comes in a standard white Treasury envelope, so it's pretty easy to spot.

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StellarSurfer

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This is super reassuring to hear from someone who just went through it! I'm actually in almost the exact same timeline - filed early February and have been stressing about this address mismatch for weeks. Quick question: when you did the ID.me verification, did you need any specific documents or was your driver's license sufficient? I'm tempted to try that route since waiting for mail always makes me nervous. Also, did the Treasury envelope have any other markings that made it obvious it was the verification letter? I live in an apartment complex and sometimes mail gets mixed up, so I want to make sure I don't miss it. Thanks for sharing your experience - it's exactly what I needed to hear!

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I dealt with this same issue about 6 months ago when I moved mid-tax season. The good news is that the IRS will send your verification letter to the address on your most recently filed return - so in your case, it should go to whatever address you used when you e-filed on February 3rd. The website showing your old address is totally normal; their online systems are notoriously slow to update and can lag behind their actual processing systems by weeks or even months. Since you filed over 2 months ago, your return should definitely be processed by now. I'd also suggest trying the ID.me verification option if you need immediate access - it's much faster than waiting for mail and doesn't depend on which address they have on file. The whole process took me about 20 minutes and I was able to access my account right away. Just make sure you have a current photo ID handy for the verification process.

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Millie Long

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Another option to look into if commuting costs are high - check if your employer offers any commuter benefits! My company lets us use pre-tax dollars for parking and public transit through our benefits program. It's not as good as a tax deduction but it does reduce my taxable income a bit.

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KaiEsmeralda

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Some companies also offer work-from-home options which can cut down commuting costs altogether. I negotiated to WFH three days a week and only commute two days. Saves me a ton on gas and car maintenance, plus I get back those hours I'd spend sitting in traffic!

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Millie Long

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That's an excellent point! Working from home even part-time can be a huge money saver. Plus, if you have a dedicated home office space that you use exclusively for work, you might qualify for the home office deduction (if you're self-employed) or other work-related expense reimbursements from your employer. It's definitely worth having that conversation with your manager if remote work is possible in your role.

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I totally feel your frustration with the commuting costs! As everyone has confirmed, those daily miles to your regular office unfortunately aren't deductible. But since you mentioned you've been doing this 3-year commute, you might want to explore some alternatives to help with those costs. One thing that helped me was calculating whether it would actually be cheaper to move closer to work or find a job closer to home. With 64 miles daily (32 each way) at current gas prices plus wear and tear, you're probably spending $4,000+ annually just on commuting costs. That's a significant chunk of money that could go toward rent in a closer location or justify negotiating remote work days. Also, keep detailed records of ANY business travel you do beyond your regular commute - even small trips to pick up office supplies or attend off-site meetings. Those miles at 67 cents each can add up to real deductions. And definitely ask HR about commuter benefits or flexible work arrangements if those are options at your company!

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Axel Bourke

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That's such a smart way to think about it! I never actually calculated my total annual commuting costs before. You're right - at 32 miles each way, I'm probably spending way more than I realized between gas, maintenance, and depreciation. The idea of moving closer or negotiating remote work days makes a lot of sense when you put it in those terms. I'm definitely going to have a conversation with my manager about working from home a few days a week. Even if I could cut my commute down to 3 days instead of 5, that would save me over $1,500 a year! Thanks for the perspective shift - sometimes you need to look at the bigger picture instead of just focusing on what you can deduct.

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