How FICA works vs federal income taxes for self-employment income
I'm trying to figure out something that should be simple but is giving me a headache. My wife and I have about $100,000 in self-employment income for the year and will be filing jointly. I understand that we need to pay self-employment tax (Medicare/Social Security) at 15.3%, but I'm confused about how federal income taxes work with this. Does the IRS calculate our federal income tax based on our full $100,000, or do they calculate it on what's left after we pay the 15.3% self-employment tax? This seems like a basic question but I can't find a clear answer anywhere. I'm trying to estimate our total tax burden for the year and this makes a significant difference.
20 comments


Adriana Cohn
The IRS applies federal income tax and self-employment tax differently, but they're both based on your total income. Here's how it works: Self-employment tax (the 15.3% for Medicare and Social Security, also called FICA when you're an employee) is calculated on your net self-employment income. That's your business income minus business expenses. Federal income tax is ALSO calculated on your total income (minus deductions and credits), not on what's left after paying self-employment tax. However, you do get to deduct half of your self-employment tax when calculating your adjusted gross income for income tax purposes. So if you have $100,000 in net self-employment income: - You'll pay self-employment tax on that $100,000 - You'll get to deduct half of your self-employment tax from your income - Then you'll calculate federal income tax on your remaining income after all deductions This is why self-employment can feel like a double tax hit - you're paying both the employer and employee portions of FICA plus income tax.
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Jace Caspullo
•So if I understand correctly, if my wife and I make $50k each from self-employment (total $100k), we'll pay 15.3% self-employment tax on the full amount, but then we get to deduct half of that when figuring out our taxable income for federal income tax purposes? Would this be calculated on Schedule SE? And does this mean I should be making quarterly estimated payments for both types of taxes?
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Adriana Cohn
•You're exactly right about the self-employment tax being applied to the full amount, and then getting to deduct half of that when calculating your income tax. This deduction happens on Schedule 1 of your Form 1040. Yes, you would calculate your self-employment tax using Schedule SE (one for each spouse who has self-employment income). The schedule will walk you through calculating the tax and the deduction. For quarterly estimated payments, you should definitely be making those if you're self-employed. Your quarterly payments should cover both your income tax and self-employment tax obligations. The IRS doesn't separate these in your estimated payments - you're simply paying toward your total tax liability. You can use Form 1040-ES to calculate your estimated payments.
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Melody Miles
After struggling with this same question last year, I found an amazing tool that answered all my self-employment tax questions. I was confused about how FICA and federal income taxes worked together and kept getting conflicting advice from friends. I discovered https://taxr.ai and it was a game-changer for my self-employment taxes. You can upload your income documents or just type your question, and it explains exactly how self-employment taxes work with your specific numbers. It showed me how the deduction for half of the self-employment tax works and gave me a clear breakdown of what I would owe. The best part is it explains everything in normal human language instead of confusing tax jargon. Seriously helped me understand how FICA vs federal income tax works when you're self-employed.
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Nathaniel Mikhaylov
•Does it actually calculate the amounts for you? Like if I input my estimated self-employment income, will it show me both the FICA and federal income tax portions? I've been using a spreadsheet but I'm not confident my formulas are right.
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Eva St. Cyr
•I'm a bit skeptical about tax tools. Does it stay updated with current tax laws? The TCJA changes are still confusing me, and I need something that's accurate for 2025 filing.
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Melody Miles
•Yes, it does calculate the actual amounts for you. You can input your expected self-employment income and any deductions, and it will show you a breakdown of both the self-employment tax (the FICA portion) and federal income tax. Much easier than trying to build your own spreadsheet with all the tax formulas. It's continuously updated with current tax laws. The developers update it whenever there are changes to tax legislation. It's definitely current with all the TCJA provisions and has the latest for 2025 filing season. I was worried about the same thing, but they keep it current with all IRS changes.
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Nathaniel Mikhaylov
I just wanted to follow up after trying https://taxr.ai that someone mentioned earlier. I've been struggling with understanding how these taxes work together for my consulting business, and it finally makes sense! I entered my projected income for the year and it broke down exactly how the self-employment tax and federal income tax would apply. It even showed me how much I'd save from that 50% self-employment tax deduction, which I didn't fully understand before. The breakdown made it super clear that I need to be setting aside more for quarterly payments than I had been. Probably saved me from an underpayment penalty! It's way better than the random calculator I was using before.
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Kristian Bishop
If you're dealing with self-employment taxes, you probably know how frustrating it is trying to call the IRS with questions. I spent WEEKS trying to get through to ask about this exact FICA vs federal tax question for my side business. Finally found https://claimyr.com which got me through to an actual IRS agent in about 15 minutes instead of waiting on hold for hours or getting disconnected. You can see how it works here: https://youtu.be/_kiP6q8DX5c The agent walked me through exactly how self-employment tax works with federal income tax and confirmed that yes, you pay SE tax on the full amount but get to deduct half when calculating income tax. They even helped me understand how to adjust my quarterly payments to account for both taxes.
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Kaitlyn Otto
•Wait, how does this actually work? Does it just call the IRS for you or something? I've been trying to get through for days about a similar question.
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Eva St. Cyr
•Sorry, but this sounds too good to be true. The IRS phone lines have been a disaster for years. I've literally never gotten through even after hours on hold. How could some random service magically get you to the front of the line?
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Kristian Bishop
•It doesn't just call for you - they have some kind of system that navigates the IRS phone tree and waits on hold for you. When they actually get through to a human at the IRS, they call you and connect you directly. You don't do any of the waiting. I was definitely skeptical too! I had tried calling the IRS four different times and never got through - either got disconnected or couldn't wait on hold any longer. I didn't believe this would work either, but I was desperate. I don't know exactly how their system works, but they got me connected to an actual IRS agent when nothing else worked. The agent answered all my questions about self-employment tax and even pulled up my account to check something about my previous quarterly payments.
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Eva St. Cyr
I need to apologize and admit I was wrong about Claimyr. After my skeptical comment, I was still desperate to talk to the IRS about my self-employment taxes, so I tried it. I still can't believe it worked. After trying for WEEKS to get through on my own, I was connected to an IRS rep in about 20 minutes. The agent confirmed everything about how FICA and federal income taxes work with self-employment income. She walked me through exactly how the 15.3% applies to my full self-employment income and then explained how I calculate my adjusted gross income after deducting half the self-employment tax. Cleared up months of confusion in one call. Seriously sorry for doubting - this service saved me from making a major error on my quarterly payments.
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Axel Far
One thing nobody mentioned yet - the 15.3% self-employment tax actually breaks down as: - 12.4% for Social Security (up to the wage base limit, which is $168,600 for 2025) - 2.9% for Medicare (no income limit) - Plus an additional 0.9% Medicare tax on income over $250,000 if married filing jointly So with $100k in self-employment income for a married couple, you'd pay the 15.3% on the full amount, but if you earned more, the Social Security portion would eventually cap out. Also, don't forget about the qualified business income deduction (Section 199A) which might allow you to deduct up to 20% of your qualified business income depending on your situation. This is separate from the self-employment tax deduction.
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Brandon Parker
•Thank you for breaking down the percentages! I didn't realize the Social Security portion had a cap but Medicare didn't. Do you know if both my wife's and my self-employment income count together toward that Social Security cap, or are they considered separately since we're each earning the self-employment income individually?
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Axel Far
•The Social Security wage base limit applies individually to each person, not to your joint return. So if you earn $60k and your wife earns $40k in self-employment income, you're both well below the $168,600 cap individually, and you'll both pay the full 12.4% Social Security tax on your respective incomes. This is different from the additional Medicare tax, which is based on your joint income for married filing jointly. But since you mentioned $100k total, you're well below the $250,000 threshold for that additional Medicare tax anyway.
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Jasmine Hernandez
Anyone have a recommendation for good tax software that handles self-employment taxes well? I've been using FreeFileWhatever but it gets confusing with all the schedules.
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Luis Johnson
•I switched to TaxSlayer last year and it was great for my self-employment stuff. It walks you through all the Schedule C questions and automatically calculates your self-employment tax. Then shows how the deduction for half your SE tax affects your federal income tax. Saved me about $300 compared to what I paid with TurboBlaster the year before.
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Sean Flanagan
Just wanted to add something that might help with the quarterly payment calculations - the IRS safe harbor rule can be really useful for self-employed folks. If you pay at least 100% of last year's total tax liability (or 110% if your prior year AGI was over $150,000), you won't face underpayment penalties even if you end up owing more at filing time. This is especially helpful when your self-employment income varies throughout the year. You can use last year's numbers as a baseline for your quarterly payments and then adjust up or down based on how your current year income is tracking. Also, remember that your quarterly payments are due on the 15th of January, April, June, and September (not every three months like you might expect). The IRS has specific due dates that don't follow a regular quarterly calendar. One more tip - if you're just starting with self-employment, consider opening a separate savings account just for taxes. I transfer about 25-30% of each payment I receive into that account to cover both the self-employment tax and federal income tax. Makes it much easier to handle the quarterly payments and avoid scrambling for cash when they're due.
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Liam O'Donnell
•This is really helpful advice about the safe harbor rule! I'm new to self-employment and didn't know about the 100%/110% rule. Quick question - when you say "total tax liability," does that include both the income tax AND self-employment tax from last year? Or just the income tax portion? Also, that tip about the separate savings account is gold. I've been just keeping everything in my main checking account and it's stressful trying to figure out how much I can actually spend vs. what I need to save for taxes. What percentage do you recommend for someone just starting out? I've heard anywhere from 25-35% depending on your income level.
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