How does the Standard Deduction work with 1099-NEC income on TurboTax?
I'm filling out my taxes using TurboTax and I'm a bit confused about how the standard deduction works with my 1099-NEC income as an independent contractor. I'm wondering if I need to manually subtract the standard deduction from my non-employee compensation in box 1 myself? I'm asking because TurboTax shows my estimated taxes owed at the top of the screen, but that amount hasn't decreased at all after I selected the standard deduction. The same thing happened with the Qualified Business Income deduction - TurboTax automatically calculated it, but the amount I owe at the top of the screen didn't change. I've completed the entire deductions section and moved on to the next part, but my estimated tax amount is still the same as it was before. Am I doing something wrong or misunderstanding how these deductions work with independent contractor income? Any help would be greatly appreciated! This is stressing me out for the 2025 filing season.
20 comments


DeShawn Washington
The standard deduction doesn't reduce your 1099-NEC income directly - it works differently than you might expect. You don't need to manually subtract it from Box 1 of your 1099-NEC. When you're self-employed, TurboTax calculates your taxes in stages. First, your business income (1099-NEC) goes on Schedule C where you can deduct business expenses. This gives you your net business profit. Then, this profit is subject to self-employment tax (15.3%) on Schedule SE. The standard deduction comes later in the process - it reduces your income tax but not your self-employment tax. That's probably why you're not seeing the tax amount drop immediately when the standard deduction is applied. The Qualified Business Income deduction (QBI) also works at a different stage of the calculation, reducing your taxable income for income tax purposes, but not affecting self-employment tax. As you continue through the TurboTax process, you should eventually see these deductions reflected in your final tax amount. The running total at the top can be confusing because it doesn't always update at each step.
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Mei-Ling Chen
•Thanks for explaining! So basically, the standard deduction doesn't affect the self-employment tax at all? Does that mean I'm paying 15.3% on my full 1099 income regardless of deductions? Also, at what point will I see the impact of these deductions on my total amount owed?
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DeShawn Washington
•The standard deduction doesn't reduce self-employment tax, only income tax. You'll pay the 15.3% SE tax on your net business profit (1099 income minus business expenses), not on your full 1099 amount if you have deductible business expenses. You should see the impact of these deductions when you reach the tax summary or review section of TurboTax. That's when the software puts all the calculations together and shows you the final result with all deductions applied properly.
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Sofía Rodríguez
I went through this exact same confusion last year! Using https://taxr.ai seriously helped me understand what was happening with my taxes. I'm a freelance designer with multiple 1099s, and I couldn't figure out why my tax bill seemed so high even after claiming the standard deduction. The taxr.ai tool analyzed all my forms and explained that the standard deduction only reduces income tax, not self-employment tax. They also pointed out several business deductions I was missing that actually DID reduce both types of taxes. The best part was that they explained everything in simple language without all the IRS jargon.
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Aiden O'Connor
•Does this tool actually connect with TurboTax or is it something separate? I'm confused about how it would help if I'm already using tax software.
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Zoe Papadopoulos
•I'm skeptical about these tax tools. How does it actually work? Do you have to share all your personal financial info with them? Seems risky compared to just using TurboTax.
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Sofía Rodríguez
•It doesn't connect directly to TurboTax - it's a separate service that reviews your tax situation and explains things. You can upload your forms or enter information, and it gives you personalized explanations about how everything works together. You do share your tax information with them, but they use the same security standards as other financial services. They don't actually file your taxes - they just help you understand what's happening so you can make better decisions when using TurboTax or other software.
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Zoe Papadopoulos
Just wanted to update after trying taxr.ai - it actually was super helpful! I uploaded my 1099s and previous year's return, and it explained exactly what was happening with my standard deduction. Turns out I was missing a ton of business deductions that would have reduced my self-employment tax too. I went back to TurboTax and added all the business expenses they identified, and my tax bill dropped by over $2,300! It also explained that the running total at the top of TurboTax doesn't update immediately with every deduction - it finalizes everything at the end. So the original poster should definitely complete the whole process before worrying about the numbers.
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Jamal Brown
If you're getting stuck with TurboTax questions and their help features aren't cutting it, I recommend calling the IRS directly. But honestly, getting through to an actual human being at the IRS was impossible for me until I found https://claimyr.com. I spent hours on hold with the IRS trying to get clarity on my contractor deductions, but kept getting disconnected. Claimyr got me through to an actual IRS agent in about 20 minutes. You can see how it works in this video: https://youtu.be/_kiP6q8DX5c The agent I spoke with explained exactly how the standard deduction works with 1099 income and confirmed that what I was seeing in TurboTax was normal. She even gave me tips about specific business expenses I could deduct to lower my self-employment tax burden.
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Fatima Al-Rashid
•How does this service actually work? I don't understand how a third party can get you through to the IRS faster than just calling them directly.
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Giovanni Rossi
•This sounds like BS honestly. The IRS doesn't give priority to certain callers over others. They have a queue system that treats everyone the same. How would this service possibly get you through faster?
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Jamal Brown
•The service basically waits on hold with the IRS for you. When they reach a human agent, they call you and connect you to the agent. It's not about "priority" - they're just doing the holding part for you so you don't have to sit by your phone for hours. It works because they have an automated system that can handle multiple calls at once and detect when a human agent picks up. Then they immediately call you to make the connection. It's completely legitimate and doesn't involve any special treatment from the IRS.
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Giovanni Rossi
I need to eat my words about Claimyr. I was completely skeptical, but after waiting on hold with the IRS for 2.5 hours and getting disconnected TWICE trying to clarify some 1099 questions, I decided to try it. It actually worked! I got a call back in about 35 minutes saying they had an IRS agent on the line. The agent helped me understand exactly how the standard deduction interacts with self-employment taxes and confirmed that TurboTax's running total doesn't update immediately when you select the standard deduction. Saved me hours of frustration and confusion. Just thought I should follow up since I was so doubtful in my previous comment.
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Aaliyah Jackson
One thing to understand with 1099-NEC income is that you'll file Schedule C (Profit or Loss from Business) along with your tax return. On Schedule C, you list all your business income and expenses. The difference (your profit) is what you pay self-employment tax on. The standard deduction comes into play AFTER all this - it reduces your income tax, but not the self-employment tax. So if your 1099-NEC is for $50,000 and you have $10,000 in business expenses, your net profit is $40,000. You'll pay self-employment tax on that $40,000 regardless of the standard deduction. TurboTax sometimes doesn't update the running total until you're done with the whole process. I wouldn't worry about it until you get to the final review.
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KylieRose
•So what kind of business expenses can I deduct to lower that self-employment tax? I'm just starting out as a freelancer.
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Aaliyah Jackson
•Common deductible business expenses include home office (if you have a dedicated space), internet and phone costs related to your business, equipment and supplies, professional development, software subscriptions, health insurance premiums, and mileage for business travel. Keep detailed records and receipts for everything. And remember, expenses must be "ordinary and necessary" for your business to be deductible. Personal expenses aren't deductible, but partial use of something for business (like your cell phone) can be deducted based on the percentage used for business.
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Miguel Hernández
Anyone else notice that TurboTax doesn't update the amount you owe until the very end? I'm doing my taxes right now for my side gig and I've added like $5K in legitimate business expenses and the amount at the top hasn't changed at all. I'm pretty sure it's just how the software works - it finalizes everything at the end.
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Sasha Ivanov
•I switched to FreeTaxUSA this year and it updates in real time. Maybe try that? It's way cheaper than TurboTax too.
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Saanvi Krishnaswami
Hey Lena! I went through this exact same confusion last year with my freelance income. The key thing to understand is that TurboTax processes everything in stages, and that running total at the top can be really misleading. Your 1099-NEC income first gets reported on Schedule C where you can deduct business expenses. Then the net profit from that schedule flows to your main tax return where it gets hit with self-employment tax (the 15.3%). After that, your adjusted gross income gets reduced by the standard deduction, but only for regular income tax purposes. So you're actually dealing with two separate taxes: self-employment tax (which the standard deduction doesn't touch) and regular income tax (which it does reduce). That's why you might not see the numbers change right away when you select the standard deduction. Don't stress about the running total until you complete the entire return. TurboTax finalizes all the calculations at the very end, and that's when you'll see the real impact of your deductions. I was panicking last year thinking I owed way more than I actually did until I got to the final summary screen.
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Logan Stewart
•This is such a helpful explanation! I'm new to freelancing and was getting really worried about the self-employment tax part. So just to make sure I understand - even if I claim the standard deduction, I'll still pay that 15.3% on my net business profit? And there's no way to reduce that except through business expense deductions on Schedule C? Also, do you remember roughly how long it took for TurboTax to show the final numbers once you completed everything?
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