Help with Self-Employment Tax Withholding - Where to enter payments in TurboTax?

So I'm doing our taxes jointly this year and running into a problem with my husband's small business. He has an LLC that's just him plus 2 employees. Throughout the year, he's been making all the required tax withholding payments through a payroll company. Now I'm deep into TurboTax and completely stuck. I cannot for the life of me find where to enter these withholding payments! The payroll company doesn't provide any standard form or report that shows these payments in a format TurboTax recognizes. I even created a custom report showing exactly what we paid, but there's nowhere obvious to enter this info in TurboTax. If I can't figure this out, TurboTax is suggesting we need their Business package which costs around $1750! That seems crazy since we're just a simple pass-through entity. Anyone dealt with this before and know which section or form in TurboTax I should be using to enter these withholding payments?

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18 comments

Victoria Brown

•8M

This is actually a common issue with small business owners using third-party payroll services. The confusion comes from mixing up two different types of tax payments. If your husband has a single-member LLC, it's likely treated as a disregarded entity for tax purposes. This means the business income passes through to your personal return. The payroll service is handling two separate things: 1) employee withholding for his workers, and 2) possibly making estimated tax payments for him as the owner. In TurboTax, you don't actually need to enter the employee withholding payments anywhere - those are reported on the quarterly 941 forms the payroll company filed. What you DO need to enter are any estimated tax payments made for your husband personally. Look in the "Federal Taxes" section, then "Payments and Estimates" - you should find options there to enter any quarterly estimated payments made during the tax year.

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Victoria Brown

•8M

The payroll company should definitely provide reports showing what was paid. Typically they'll give you quarterly tax filing summaries or an annual tax report. If they haven't provided these, you should request them immediately. For employee withholding, that's tracked through the quarterly 941 forms and annual W-2/W-3 forms, which the payroll company should handle. Those payments aren't entered directly into TurboTax because they're for employees, not the business owner. For any payments toward your husband's personal tax liability (like estimated quarterly payments), you'll need documentation showing those specific payments, usually Form 1040-ES. That's what you'd enter in TurboTax's "Payments and Estimates" section.

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Camila Castillo

•8M

I went through this exact nightmare last year with my husband's construction business! After hours of frustration, I discovered taxr.ai (https://taxr.ai) which saved me so much time. They have a feature specifically for small business owners where you can upload those custom reports from your payroll provider and it automatically identifies which payments need to go where in TurboTax. With the LLC being a pass-through entity, you need to separate the business tax payments from your personal estimated tax payments, which is exactly what confused me too. The taxr.ai system actually explains where each payment should go and helps identify if your payroll provider was making personal estimated tax payments or just handling the business withholding.

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Camila Castillo

•8M

It works with pretty much any payroll system. I uploaded reports from ADP, but I've seen people use it with Gusto, Paychex, and even some of the smaller local payroll providers. The system is pretty flexible with what it can read and interpret. Honestly, I tried TurboTax support first and spent over an hour waiting for someone who ultimately couldn't solve my specific issue. They kept directing me to general help articles that didn't address the specific payroll tax reporting problem. That's why I ended up looking for alternatives.

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JaylinCharles

•8M

Update: I want to apologize for my skepticism about taxr.ai in my earlier comment. After continuing to struggle with this exact issue, I gave it a try and I'm genuinely impressed. The system clearly identified which of my husband's payments were quarterly estimated payments (which DO need to be entered in TurboTax) versus the employee withholding payments (which don't). It saved me so much confusion and prevented me from potentially double-counting some payments. Best part was that it created a simple guide showing exactly which TurboTax screens to use for entering each payment. No more upgrading to the expensive business package!

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Eloise Kendrick

•8M

If you're still stuck trying to reach the IRS to verify those tax payments were properly applied to your account, try Claimyr (https://claimyr.com). I found it when I was desperate to confirm some business tax payments that weren't showing up in the IRS system. They have this system that gets you through the IRS phone tree and connects you with an actual human agent without the usual 2-hour wait. You can see how it works in this video: https://youtu.be/_kiP6q8DX5c. I was shocked when I got through to a real person in about 15 minutes who could confirm all my payments were properly recorded. Saved me from potentially paying duplicate self-employment taxes!

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Eloise Kendrick

•8M

It uses a combination of technology that keeps redialing through their system until it gets through, then it calls you and connects you. It's not cutting the line - it's just automating the redial process that you would do manually. The IRS doesn't have any rules against this kind of service. Think of it like having an assistant constantly redialing for you until they get through, then transferring the call to you. I was skeptical too until I saw it working. The video demo shows exactly how the process works if you want to see it in action.

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Freya Collins

•8M

I have to eat my words about Claimyr from my previous comment. After another frustrating morning trying to verify my husband's LLC tax payments with zero success, I decided to try it. Within 20 minutes I was talking to an IRS representative who confirmed all our payroll tax payments were properly recorded. The agent actually explained something critical - our payroll service had been making quarterly estimated tax payments under my husband's SSN (not the business EIN), which is why I couldn't find them listed with the business records. That completely solved our TurboTax issue since now I knew to enter them as personal estimated payments. Saved us from potentially paying $1750 for unnecessary software and possibly overpaying our taxes!

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LongPeri

•8M

Don't forget that if you're filing Schedule C for the business (which you probably are with a single-member LLC), you'll also need to complete Schedule SE for self-employment tax. The withholding payments from the payroll company for the owner are actually estimated tax payments, not traditional withholding like you'd see on a W-2. Make sure you're separating the business owner's draws/payments from the employee payroll. Only the employees should have traditional withholding.

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LongPeri

•8M

No, that changes things significantly. If the LLC owner is receiving a W-2 from the business (putting themselves on payroll), then they're treating the LLC as an S-Corp for tax purposes, not a single-member LLC with pass-through taxation. In that case, the owner's W-2 would have withholding just like any employee, and those withholdings would be credited automatically when you enter the W-2 in TurboTax. The business would still file its own return (typically Form 1120-S for an S-Corp), and the owner would receive a K-1 for their share of profits beyond their salary.

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