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Payroll software for self-employed professionals
No credit card required. Cancel anytime.
The simplest way to put yourself on payroll and stay compliant
If you're self-employed, paying yourself shouldn't mean wrestling with IRS forms. FreshBooks makes payroll for self-employed business owners straightforward. Set your salary, run payroll, and let your federal and state taxes file themselves while you focus on the business.
Pay yourself in minutes, without hassle
Fast, easy setup
Put yourself on payroll the same day. Guided onboarding walks you through your EIN, W-4, bank, and state tax details.
Reasonable salary, done right
Set your own salary, run it on schedule, and let FreshBooks calculate, pay, and file your federal and state payroll taxes—941s, 940s, and W-2s included.
Payroll and accounting in one login
Every pay run posts straight to your chart of accounts. Say goodbye to CSV exports, manual reconciliations, and bloated tools.
Built for self-employed business owners
Single-member LLCs electing S-corp status
Pay yourself a reasonable salary and keep the IRS happy.
Sole proprietors paying themselves a W-2 salary
Move from guesswork to a real paycheck.
Freelancers and consultants scaling to full business ownership
Grow from freelancing and side gigs to a proper business with payroll.
Self-employed owners adding a first W-2 employee or contractor
Pay yourself and your first hire from the same place, without complexity.
S-corp salary compliance without the guesswork
No more chasing quarterly deadlines
Every pay run in the books, in real time
S-corp salary compliance without the guesswork
No more chasing quarterly deadlines
Every pay run in the books, in real time
S-corp salary compliance without the guesswork
No more chasing quarterly deadlines
Every pay run in the books, in real time
Set up payroll for self-employed professionals in 6 steps
Create your FreshBooks account—free for 30 days, no credit card needed.
Select the Payroll tab, then click Set Up Payroll under FreshBooks Payroll powered by Gusto.
Enter EIN and bank information.
Onboard yourself and your employee with a W-4 and pay rate.
Set up state tax for your business.
After verification, run your first payroll.
Find the right FreshBooks plan for your business
Choose a plan and run your business with smarter tools. Risk-free. 30-Day money-back guarantee.
Plus
The ROI of running your whole business in FreshBooks
Take back 11 hrs a week
Spend less time on admin and more on the work that grows your business
Save up to $580 a month
Capture every billable minute and stop money slipping through the cracks.
Track 365 days of tax info
Year-round records mean filing is quick and painless when it counts.
Why Business Owners Love FreshBooks
FreshBooks has really helped me to be more efficient throughout the year so that tax time…it’s less stressful
Damona Hoffman
Dear Mrs D, Inc.
FreshBooks has really helped me to be more efficient throughout the year so that tax time…it’s less stressful
Damona Hoffman
Dear Mrs D, Inc.
DIY payroll vs. FreshBooks Payroll for self-employed business owners
| DIY payroll (spreadsheet and IRS forms) | FreshBooks Payroll |
|---|---|---|
Stay compliant as rules change | You track the changes | Handled for you |
| You do the math and own the errors | Calculated automatically |
Direct deposit | Not possible without a separate service | Included |
| On you, every quarter and year-end | Filed for you |
| Not possible without a separate service | Included |
| Manual CSV uploads | Syncs automatically |
| Forums and guesswork | Real human help when you need it |
Running payroll by hand with a spreadsheet and IRS forms can seem like a money-saver when you're only paying yourself. But it leaves the hard parts to you—setting a defensible salary, calculating withholdings, and filing 941s, 940s, and W-2s on time.
For an S-corp owner, one compliance slip can mean penalties that dwarf any savings.
FreshBooks Payroll is a better alternative for self-employed owners. It calculates, pays, and files your federal and state payroll taxes automatically, runs your owner salary on schedule, and posts every pay run straight to your books—no CSV exports or reconciliations.
On top of that, you get secure data storage and award-winning support whenever you're stuck. FreshBooks gives you everything you need to pay yourself and stay compliant with confidence.
A powerful partnership
You’re in good company
Rest easy knowing your payroll is in good hands. FreshBooks partners with Gusto to offer speedy set up and pleasant pay days. All from the comfort of your FreshBooks account.
Keep your books in sync
Transactions for every pay run will be automatically created so your reports and books stay accurate and organized.
See pay run info
Get an at-a-glance summary of your previous payroll runs with hours and earnings for your team.
File payroll taxes automatically
With FreshBooks Payroll, your payroll taxes are automatically filed.
Resources to support small business owners
8 Best Payroll Software for Small Business (2026)
How to Do Payroll Yourself for Small Business
How to Set Up Payroll for Your Small Business in 6 Easy Steps
Frequently Asked Questions
