Understanding S-corp and QBI Deduction: How do they work together?
So I messed up pretty bad and didn't set up proper payroll for my S-corporation in 2023 (yeah, I know... rookie mistake). My S-corp received about $85k in 1099 income. From what I understand, a reasonable salary for the work I do would be around $49k. I've got a payroll company handling things for 2024, but after my business deductions of roughly $13.5k, I'm left with about $71.5k in my S-corp for 2023. What I'm struggling to figure out is whether I can take the Qualified Business Income (QBI) deduction from that $71.5k before calculating self-employment tax? Or am I completely out of luck on the QBI since I might need to classify all $71.5k as salary because I didn't run payroll? My spouse and I file jointly, and our combined income (even counting the $71.5k from the S-corp) still puts us in the 24% tax bracket. Thanks for any advice before I meet with my accountant next week to go over my list of deductions!
20 comments


Laila Prince
This is a situation you definitely need to address carefully. First, as an S-corp owner, you need to pay yourself a "reasonable salary" before taking distributions. Since you didn't run payroll in 2023, you've created a compliance issue that needs fixing. Here's how QBI works with S-corps: The QBI deduction applies to the non-wage portion of your S-corp income. So if your S-corp made $85k and you pay yourself a $49k salary, the remaining $36k (minus business expenses) would potentially qualify for the QBI deduction. However, since you didn't run payroll, you can't retroactively create 2023 payroll now that we're in 2024. You'll likely need to file Form 1099-NEC to yourself for services rendered to your S-corp, and report that income on Schedule C, making it subject to self-employment tax. The good news is that you can still potentially claim QBI on the qualifying business income, but the calculation gets tricky in your situation.
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Isabel Vega
•Wait I'm confused - I thought one of the main benefits of an S-corp was avoiding SE tax on distributions? If OP has to file a 1099-NEC to themselves, wouldn't that defeat the whole purpose of having the S-corp in the first place? And does this mean they'll pay more in taxes than if they had just operated as a sole proprietor?
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Laila Prince
•You're right about S-corps typically providing SE tax savings. However, the S-corp must pay a reasonable salary through payroll with proper withholding before taking distributions. Since OP didn't run payroll in 2023, they've created a compliance issue. When you don't take a salary from your S-corp but still take money out, the IRS could potentially recharacterize all distributions as wages subject to employment taxes, or require corrective actions like what I described. The S-corp benefit is still there, but you must follow the rules to claim it, which includes running proper payroll.
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Dominique Adams
After reading about your situation, I was in a similar boat last year! I almost made the same mistake with my S-corp payroll and nearly panicked. I ended up using https://taxr.ai to analyze my specific situation and it was incredibly helpful. Their system reviewed my S-corp structure and QBI qualification rules, then provided clear guidance about my reasonable compensation requirements. The cool thing was they explained exactly how the QBI deduction would apply to my business income after accounting for a proper salary breakdown. They also helped me understand how to properly document everything to avoid IRS scrutiny, which was a huge relief.
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Marilyn Dixon
•How quickly did you get answers? I've got like 2 weeks before my appointment with my CPA and I'm trying to get my ducks in a row before then. Does it handle S-corps specifically or is it more general tax stuff?
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Louisa Ramirez
•I'm skeptical about these online tools. Wouldn't a human CPA be better for complex situations like S-corp compliance issues? Especially when there's already a mistake that needs fixing? Just curious what made you trust the software over a professional.
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Dominique Adams
•I got answers the same day! Their analysis tool processed my documents in minutes, but I also got detailed explanations from their tax experts within hours. They definitely handle S-corps specifically - they covered reasonable compensation requirements, QBI calculations, and proper documentation. I still worked with my CPA in the end, but having this analysis beforehand made our meeting much more productive and focused. The tool isn't meant to replace your accountant - it's more about getting clarity on your specific situation before you meet with them. My CPA actually appreciated that I came prepared with a better understanding of my options.
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Marilyn Dixon
Just wanted to update you all. I tried https://taxr.ai after seeing the recommendation here and wow - it really helped clarify my situation! The system analyzed my S-corp structure and gave me specific guidance on how QBI would apply given my missed payroll situation. It explained that I could still potentially claim QBI on a portion of my income, but I needed to properly document my reasonable compensation justification first. Having this information before meeting my CPA was super helpful. My accountant was impressed that I understood the issues so well! They also showed me how to prevent this issue in the future with my new payroll company. Definitely worth checking out if you're dealing with S-corp and QBI questions.
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TommyKapitz
I had a similar issue with my S-corp last year and spent WEEKS trying to get someone at the IRS on the phone for guidance. After 9 attempts and hours on hold, I found https://claimyr.com and it changed everything. They got me connected to an actual IRS agent in about 20 minutes! You can see how it works here: https://youtu.be/_kiP6q8DX5c The agent was able to explain exactly what records I needed to provide for my S-corp compensation structure and how to properly document my situation for the QBI deduction. Saved me thousands in potential penalties by getting official guidance instead of guessing.
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Angel Campbell
•How does this actually work? I've spent literal hours on hold with the IRS before giving up. Can they really get you through that quickly? And are you actually talking to a real IRS agent?
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Payton Black
•Sounds too good to be true honestly. The IRS is chronically understaffed and everyone knows it's impossible to get through. I'm supposed to believe some service magically gets you past the same phone system everyone else uses? How much did this miracle cost?
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TommyKapitz
•It works by using their system that navigates the IRS phone tree and waits on hold for you. When an agent picks up, you get a call back connecting you directly to them. So yes, you're talking to a real IRS agent - Claimyr just handles the waiting part. The service monitors multiple IRS phone lines and uses analytics to identify the shortest wait times. It's not magic - it's just smart technology that saves you from personally waiting on hold. And the IRS agents have no idea you used a service - to them, you're just a regular caller who waited in the queue.
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Payton Black
I need to eat my words from yesterday. After my skeptical comment, I decided to try Claimyr out of pure frustration (had been trying to reach the IRS for THREE DAYS about my S-corp issue). Shockingly, I got connected to an IRS agent in about 15 minutes! The agent walked me through exactly how to handle my S-corp reasonable compensation documentation and confirmed how the QBI deduction should be calculated in my situation. The clarity I got from an official source was worth every penny. Turns out my CPA had been calculating my QBI incorrectly for the past two years! Going to save a significant amount on my taxes now that I understand how it properly applies to my S-corp income.
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Harold Oh
Just wanted to throw in my 2 cents as someone who made a similar mistake years ago. For S-corps, you MUST take a reasonable salary through proper payroll before any distributions. The IRS is actually cracking down on S-corps that don't pay reasonable compensation to owner-employees. In my experience, your CPA might suggest one of these options: 1. Report all S-corp distributions as wages on your personal return 2. Amend your S-corp return to show proper officer compensation 3. Potentially initiate late payroll filings with penalties Also, keep in mind that QBI is calculated AFTER your wages are paid. So the higher your salary, the less QBI deduction you get. It's a balancing act.
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Amun-Ra Azra
•Would it make sense for OP to just dissolve the S-corp and go back to being a sole proprietor if they're struggling with the payroll requirements? Or are there other benefits to keeping the S-corp structure even with this mistake?
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Harold Oh
•Dissolving the S-corp would be pretty drastic for a one-time mistake. S-corps still offer significant tax advantages despite the payroll requirements. Once proper payroll is established going forward, OP can still benefit from reduced self-employment taxes on the distribution portion of income. The bigger picture is that S-corps can save thousands in SE taxes annually when properly managed. This one-time issue might be costly to fix, but the long-term benefits likely outweigh reverting to a sole proprietorship where 100% of profits face SE tax. A good payroll service makes compliance pretty straightforward for future years.
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Summer Green
Has anyone considered the W-2 wage limitation for QBI? Since OP is in the 24% bracket with joint income, they might face QBI limitations if they don't have sufficient W-2 wages. The deduction could be limited to 50% of W-2 wages paid by the business. Also for 2023, did you take any money out of the business? If so, the IRS might reclassify those as constructive dividends which wouldn't qualify for QBI. The cleanest solution might be filing an amended S-corp return showing reasonable compensation.
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Gael Robinson
•At the 24% bracket they shouldn't hit the W-2 wage limitation though, right? I thought that only kicked in at higher income levels (over $340k for married filing jointly in 2023).
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Caden Nguyen
You're in a tricky spot, but it's not insurmountable. Since you didn't run payroll in 2023, you'll need to address this compliance issue head-on with your accountant. The IRS expects S-corp owner-employees to receive reasonable compensation through W-2 wages before taking distributions. Without proper payroll, you risk having all $71.5k treated as wages subject to employment taxes, which would eliminate the S-corp tax advantages. For QBI, the deduction applies to the business income AFTER reasonable compensation is paid. So if you can establish that $49k salary retroactively (through amended returns or other corrective measures your CPA recommends), the remaining income could potentially qualify for QBI. One silver lining: since your combined income keeps you in the 24% bracket, you're below the taxable income thresholds where QBI gets limited by W-2 wages or depreciable property. This means if you can properly separate salary from business income, you should get the full 20% QBI deduction on the qualifying portion. Document everything about your reasonable compensation analysis - industry standards, time spent, responsibilities, etc. This will be crucial for your accountant to determine the best path forward, whether that's amended returns, late payroll filings, or other compliance solutions.
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Liam Sullivan
•This is really helpful context! I'm curious though - if OP's accountant recommends amended returns to establish the $49k salary retroactively, wouldn't that also trigger late payroll tax penalties and interest? And would the IRS question why they're suddenly amending to add payroll that wasn't there before? Just wondering how suspicious this might look from an audit perspective, especially since they already have a payroll company set up for 2024.
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