Nonprofit Payroll Software
Automate payroll, streamline contractor payments, and more
Nonprofit Payroll Software Made Simple
Loved by small and large nonprofits, charities, and foundations
Handle Tax Exemptions
Juggle Multiple Pay Rates
Free USA-based Support
Key Payroll Features for Nonprofit Organizations
Pay Contractors in Payroll
Pay contractors with employees on the same payroll.
Employee Self-onboarding
Reduce your admin work by letting new hires self-onboard.
Auto Payroll
Set it up once, and payroll runs itself!
Health Benefits
Find affordable health, dental, and vision insurance from major carriers through SimplyInsured.
Payroll That Respects Your Budget
Nonprofit budgets are tight, and staff time is tighter. Patriot's Basic Payroll is $17/month + $4 per worker paid, and Full Service Payroll is $37/month + $5 per worker paid, so you can run accurate payroll without hiring a payroll specialist or pulling an administrator away.
No hidden fees
Transparent pricing without needing to call for a quote.
No payroll experience required
Payroll built for staff who wear multiple hats, not payroll experts.
Top-notch value
Affordable payroll so you can spend less on admin work and more on your nonprofit’s mission.
Nonprofit Payroll Tax Compliance, Simplified
Running payroll for a tax-exempt organization comes with rules that don't apply to typical businesses, and getting them wrong can mean overpaying taxes or missing filings. With Patriot’s payroll software, you can easily mark your nonprofit as exempt from FUTA and SUTA taxes, if applicable, and the system won’t calculate these taxes when you run payroll.
Churches have their own set of rules, too; see our church payroll software for specific information.
Fast, Easy Payroll for Your Nonprofit Organization
As a very small nonprofit organization, I have really appreciated the comprehensive payroll support. I never have to worry about whether tax reports are being filed on time or correctly, and when something new comes along in the payroll world, Patriot Software is always right on top of the changes and makes it simple for our organization to comply with new regulations. This is the most user-friendly payroll software system I've ever used.”
-High Plains Housing Dev
Trusted by Nonprofit Organizations Nationwide
Nonprofit Payroll Resources
Ready to Simplify Your Nonprofit Organization’s Payroll?
Frequently Asked Questions
Setting up payroll for a nonprofit is similar to any small business: you'll need your Employer Identification Number (EIN), state tax IDs, and employee details like names, addresses, and Social Security numbers. Patriot Software’s setup wizard walks you through entering this information, plus any 501(c)(3) tax-exempt status details, so your payroll is configured correctly from day one.
As a nonprofit, you may prioritize affordable and easy-to-use payroll software. Patriot’s user-friendly payroll platform is easy to learn and use, plus affordable, making it a top choice for nonprofits nationwide.
Yes! Rest easy with free USA-based support available via phone, chat, or email. We’re here to help your nonprofit run payroll quickly and get back to your mission.
If your nonprofit doesn't run payroll in a given month (common for seasonal staff or volunteer-heavy organizations) you'll only be charged Patriot's base monthly price, not the per-worker fee. This makes Patriot Software a budget-friendly option for nonprofits with fluctuating staffing needs throughout the year.
No, 501(c)(3) nonprofits are not exempt from all payroll taxes. They must still withhold and pay Social Security and Medicare (FICA) taxes just like for-profit employers. However, qualifying 501(c)(3) organizations are exempt from FUTA tax and possibly SUTA tax. Patriot Software won’t calculate taxes you mark as exempt from when you run payroll.
The Federal Unemployment Tax Act (FUTA) generally requires employers to pay 6% on the first $7,000 of each employee's annual wages. Qualifying 501(c)(3) nonprofits are exempt from this tax. In Patriot Software, you can mark your organization as FUTA-exempt, and the system automatically excludes that calculation from every payroll run.
The IRS requires employers, including nonprofits, to retain payroll records for at least four years. Required records include employee names and Social Security numbers, wages paid, tax withholdings, and pay dates. The Department of Labor requires that employers to retain payroll records for at least three years and records on which wage computations are based (e.g., wage rate tables) for two years. Patriot Software automatically stores payroll data, making it accessible whenever you need it.