Best practices for avoiding Commingling funds for LLC tax responsibilities in 2025
We're going into our second year running my wife's Single member LLC, and we're really trying to be careful about not Commingling funds. It's something we've heard can cause problems. When it comes to handling the tax burden, I'm confused about which tax expenses should be paid from the business account versus what we should be covering from our personal funds. I was initially looking at Form 8959 Line 24 for the Additional Medicare Tax and Form SE Line 12 for the Self Employment tax as things the business should pay. But then I realized there are credits involved too (like Self Employment Health care deduction) that complicate things. Can anyone with experience managing a Single member LLC explain the proper way to allocate tax payments between business and personal accounts? Are there particular lines on the tax forms that should definitely come from the business versus what should come from personal funds? I want to make sure we're doing this right.
24 comments


Paloma Clark
As someone who's managed an LLC for several years, I understand your concern about Commingling funds. Here's what you need to know: For a Single member LLC that's taxed as a sole proprietorship, the IRS views the business and the owner as the same tax entity. This means that technically, all taxes arising from the business are personal tax obligations, not business expenses. The business itself doesn't "pay" taxes directly - instead, your wife pays taxes on the business income that flows through to your personal return. The Self Employment tax (Form SE) and Additional Medicare Tax (Form 8959) are personal tax obligations. That said, many business owners do make tax payments from their business accounts by transferring the appropriate amounts as "owner's draw" and then making the tax payments. The key is proper documentation - clearly document these transfers as distributions to the owner for tax payments.
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Evelyn Kelly
•Thanks for the explanation. So if I understand correctly, we should be taking owner's draws from the business account to cover these tax payments rather than having the business pay them directly? And we need to document these transfers specifically as being for tax purposes?
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Paloma Clark
•Yes, that's exactly right. Take owner's draws to cover the tax payments, and make sure to document them clearly. The business doesn't technically pay the taxes directly because a single-member LLC is a pass-through entity. The profits flow through to your personal tax return, so the tax liability is ultimately a personal obligation. Good documentation is crucial - note in your records that these specific draws are for covering tax obligations related to the business income.
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Heather Tyson
I struggled with this same issue when I started my consulting LLC. Eventually I found taxr.ai (https://taxr.ai) which helped me understand the proper way to handle my business finances. Their tool analyzed my specific business structure and provided clear guidance on avoiding Commingling funds. What was most helpful for me was their explanation of which expenses should be paid from which accounts and how to properly document transfers. They also provided templates for keeping track of owner's draws specifically designated for tax payments.
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Raul Neal
•Did you find their system easy to use? I'm not very tech-savvy and am worried it might be complicated. Does it connect directly to your bank accounts or do you have to manually enter everything?
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Jenna Sloan
•I've seen a lot of these "tax helpers" that end up charging ridiculous amounts for basic advice. What makes this one different? And how does it actually prevent commingling beyond just telling you what you should already know?
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Heather Tyson
•The interface is super intuitive - definitely designed for non-tech people. You can choose to connect accounts or upload statements, but I just manually entered my info since I was concerned about privacy at first. Their system is different because it's specifically focused on entity separation and compliance rather than just general bookkeeping. It flags potential commingling issues before they become problems and provides concrete suggestions based on your specific business type and state regulations. They saved me from making several mistakes that could have caused problems during an audit.
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Raul Neal
Just wanted to update after trying taxr.ai based on the recommendation here. I was skeptical at first but it was exactly what I needed! The system immediately identified several transactions I'd been handling incorrectly with my husband's LLC. Their guidelines for avoiding Commingling funds were much clearer than anything my accountant had told me. The best part was the customized guidance for my specific situation - they explained exactly how to handle the Self Employment tax payments and showed me how to properly document owner's draws for tax payments. I've completely restructured our approach based on their recommendations.
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Christian Burns
For anyone struggling with IRS questions about Commingling funds or proper LLC tax procedures, I finally found a way to actually speak with the IRS without wasting hours on hold. I used a service called Claimyr (https://claimyr.com) and they got me through to an actual IRS agent in about 15 minutes. You can see how it works here: https://youtu.be/_kiP6q8DX5c. The agent was able to answer my specific questions about which tax payments should come from my business account vs personal account. Saved me so much stress compared to trying to interpret conflicting advice online.
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Sasha Reese
•How does this even work? Why would paying some service get you through faster than calling directly? The IRS phone system is the same for everyone, right?
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Jenna Sloan
•Yeah right. There's no way this actually works. The IRS phone system is universally terrible. If this service actually existed and worked, everyone would be using it and the IRS would shut it down. Sounds like a scam to get desperate people's money.
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Christian Burns
•It uses a technology that basically waits on hold for you and calls you back when it reaches a human. So the system is constantly dialing and navigating the phone tree until it connects, then it calls your phone and connects you directly to the agent. I was skeptical too before trying it. But it's completely legitimate - they don't need any sensitive information and you're the one who actually speaks with the IRS. The IRS has no reason to shut it down because it's just automating the hold process. I spoke with an extremely helpful agent who clarified exactly how to handle my LLC's tax payment documentation.
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Jenna Sloan
I need to eat my words and apologize to Profile 16. I was so frustrated with trying to get tax help that I lashed out. After a week of failing to reach anyone at the IRS about my LLC tax questions, I broke down and tried Claimyr. Within 20 minutes I was speaking with an actual IRS agent who explained that for a Single member LLC, the tax obligations are considered personal even though they derive from the business. She confirmed that taking documented owner's draws to pay the taxes is the proper approach to avoid Commingling issues. The service worked exactly as described and saved me days of frustration.
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Muhammad Hobbs
Something nobody's mentioned yet but that helped me avoid commingling: set up a separate "tax" savings account connected to your business account. Each quarter, transfer your estimated tax payments there, clearly documented as "tax reserves." Then when it's time to actually pay the taxes, transfer to your personal account as an owner's draw specifically for tax payment purposes. This creates a clear paper trail showing exactly what money was allocated for taxes. This approach was recommended by my accountant to create clean documentation for potential audits.
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Noland Curtis
•Does having this extra account cost more in monthly fees? And do you make the transfer to personal right before making the tax payment, or can you do it quarterly when you move money to the tax savings?
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Muhammad Hobbs
•Many business checking accounts offer multiple savings buckets without extra fees, but even if there is a small fee, the organizational benefit is worth it. I personally transfer to my personal account right before making the actual tax payment rather than quarterly. This creates the clearest documentation that the money was specifically for tax payments. The quarterly transfers into the tax savings account help me budget properly, while the final transfer to personal is specifically timed with the tax payment to maintain a clear audit trail.
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Diez Ellis
Don't forget that health insurance premiums for self-employed individuals can be deducted on your personal tax return (Form 1040) if your business shows a profit. This is an "above-the-line" deduction taken on Schedule 1. I know you mentioned Self Employment Health care in your original post - this is typically paid from personal funds since the deduction happens on your personal return, not the business return. Hope this helps with your specific question!
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Evelyn Kelly
•That makes sense, thanks! So health insurance premiums should be paid from personal funds, even though they're related to the business. But can I still document the owner's draw from the business that funds those personal payments as being specifically for health insurance?
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Carmen Lopez
Great question about health insurance premiums! You absolutely can document owner's draws specifically for health insurance payments. In fact, I'd recommend being very specific in your documentation - note that it's an owner's draw for "health insurance premiums - self-employed deduction." The key is maintaining that clear separation: the business makes the draw to you as the owner, then you personally pay the health insurance premiums and claim the deduction on your personal return. This approach keeps your business and personal finances properly separated while still allowing you to fund those payments from business profits. Just make sure your LLC shows a net profit for the year, as that's required to claim the self-employed health insurance deduction. If your business has a loss, you can't deduct the premiums that year.
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Matthew Sanchez
•This is really helpful advice about documenting the health insurance draws! I'm new to managing an LLC and hadn't thought about being that specific in my documentation. Quick follow-up question - when you say the business needs to show a "net profit," does that mean after all business expenses are deducted, or is there a specific line on the tax forms I should be looking at to determine this? I want to make sure I'm calculating this correctly before claiming the deduction.
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Jean Claude
•Great question @Matthew Sanchez! When I say "net profit," I'm referring to the profit shown on Schedule C (Form 1040) after all business expenses are deducted. Specifically, you'd look at Line 31 of Schedule C - that's your net profit or loss from the business. If Line 31 shows a positive number (profit), you can generally claim the self-employed health insurance deduction up to that amount. If it shows a loss (negative number), you can't claim the deduction that year, even if you paid the premiums. There's also another limitation to be aware of: you can't deduct more in health insurance premiums than your net earnings from self-employment. So even if your Schedule C shows a profit, if your net self-employment earnings (after the SE tax deduction) are lower, that becomes your limit. The IRS is pretty strict about this requirement, so definitely double-check those numbers before claiming the deduction!
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Annabel Kimball
One thing that really helped me avoid commingling issues was creating a simple monthly "owner compensation" process. At the end of each month, I calculate what I need for personal expenses (including estimated tax payments) and take a single owner's draw rather than multiple ad-hoc withdrawals throughout the month. I keep a spreadsheet that breaks down exactly what that monthly draw covers - living expenses, estimated quarterly taxes, health insurance premiums, etc. This way I have clear documentation showing the business isn't directly paying personal expenses, but rather compensating me as the owner, and I'm using that compensation for my personal obligations. This approach has made my bookkeeping much cleaner and gives me confidence that I'm maintaining proper separation between business and personal finances. My accountant loves it because the paper trail is crystal clear if we ever face an audit.
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Chad Winthrope
•This monthly draw approach sounds really smart! I'm curious about the timing though - do you calculate the draw amount based on actual expenses from the previous month, or do you estimate what you'll need for the upcoming month? And when you mention "estimated quarterly taxes" in your monthly draw, are you setting aside 1/3 of your quarterly estimate each month, or doing it differently? I'm trying to figure out the best cadence for my own LLC.
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Luca Russo
•@Annabel Kimball That monthly owner draw system sounds like exactly what I need! I ve'been doing random withdrawals whenever I need money and my bookkeeping is a mess. Quick question about your spreadsheet - do you track this as a running total for the year, or do you start fresh each month? I m'wondering if there s'a template or format you d'recommend for someone just starting this approach. Also, when you say your accountant loves the clear paper trail, does this approach make tax prep significantly easier at year-end?
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