Compare payroll software for nonprofits managing W-2 staff, grant-funded positions, and optional 1099 consultants or contractors.
Nonprofits need payroll that handles W-2 staff—program, admin, and grant-funded positions—plus 1099 consultants or contractors when you use them. Labor cost that ties to programs, grants, or projects matters for reporting and fund accounting when you use QuickBooks or similar. Our picks work for small and growing organizations, whether you want an all-in-one platform or simple flat-rate payroll that syncs with your books.
Our top payroll picks for nonprofits.
Best overall for small nonprofits4.8From $40/moAll-in-one payroll with multiple pay rates, automatic tax forms, and built-in time tracking. Handles W-2 and 1099 in one system. No sales cycle—good for executive directors and office managers running payroll.
Best for nonprofits using QuickBooks4.6From $30/moPayroll inside QuickBooks so labor cost flows into your books and reporting. Ideal when you run books in QuickBooks. Pay staff and 1099 in the same system; time tracking can tie hours to programs, grants, or classes.
Best value for straightforward payroll4.5From $40/moFlat pricing and one plan. Pay W-2 employees and 1099 contractors with tax forms included. Simple for small teams—works with any accounting software. Support included.
Best for growing nonprofits4.4From Custom pricingPayroll and HR that scale to more staff and locations. Custom pricing and optional dedicated support. Good when you're expanding and want a full-service partner for compliance and multi-state.
Side-by-side at a glance.
| Software | Best for | Starting price | Payroll types | Standout feature | Review |
|---|---|---|---|---|---|
| Gusto | Best overall for small nonprofits | $40/mo | W-2, 1099 | Time tracking; multiple rates; all-in-one | Read review |
| QuickBooks Payroll | Nonprofits using QuickBooks | $30/mo | W-2, 1099 | Labor cost by program/grant; job costing | Read review |
| OnPay | Best value; straightforward payroll | $40/mo | W-2, 1099 | Flat pricing; 1099 included | Read review |
| ADP | Growing nonprofits | Custom pricing | W-2, 1099, multi-state | Scale; optional dedicated support | Read review |
What to look for when you're choosing payroll as nonprofits.
Nonprofits often have W-2 staff (program, admin, grant-funded) plus 1099 consultants or contractors for projects, audits, or specialty work. Your payroll system should handle both in one place—correct withholding for W-2, no withholding for 1099, and the right tax forms (W-2 vs 1099-NEC) at year-end. Contractor self-service lets 1099s view pay stubs without extra admin.
Allocating labor cost by program, grant, or project is central to nonprofit reporting and funder requirements. If you run your books in QuickBooks, payroll that posts labor to jobs or classes (QuickBooks Payroll) keeps program and grant costing accurate. Gusto and OnPay sync to QuickBooks but don't push cost to jobs the same way; they're still strong for running payroll—you can allocate in your chart of accounts or fund accounting tool.
Staff hours—by program or grant—can be captured with time tracking, timesheets, or manual entry. The best setup syncs hours into payroll so you're not re-entering data. Gusto has built-in time tracking; QuickBooks Payroll integrates with QuickBooks Time for time-by-job. Accurate hours support grant reporting and labor allocation.
Nonprofits with staff in more than one state need payroll that handles multi-state tax registration, filing, and compliance. All of our picks support multi-state; ADP adds dedicated support when you have more complexity or locations.
Many nonprofits have an executive director or office manager running payroll. Choose software that's straightforward to set up and run—published pricing, no long sales cycle, and support when you need it. Gusto and OnPay are built for self-serve; QuickBooks Payroll fits if you already use QuickBooks; ADP offers dedicated support when you're ready to scale.
Why we chose these tools for nonprofits.
Gusto is our top pick for most small nonprofits: W-2 and 1099 in one system, automatic tax forms, and built-in time tracking. No sales cycle—executive directors and office managers can run payroll and add contractors without calling a rep. It scales as you add staff and programs.
When you run books in QuickBooks, QuickBooks Payroll keeps payroll and labor cost in the same system. Labor posts to jobs or classes for program and grant costing—critical for nonprofit reporting. Pay staff and 1099 in one place. Best if QuickBooks is already your central tool.
OnPay offers straightforward payroll for W-2 and 1099 at a flat price. One plan, no tier maze—good for nonprofits that want predictability. Contractor payments and tax forms are included. Works with any accounting software.
ADP fits growing nonprofits that want scale and optional dedicated support. Multi-state payroll, more staff, and a full-service relationship when you need it. Custom pricing—get a quote and compare to Gusto or OnPay at your headcount.
For more options across all use cases, see our best payroll software roundup. To compare platforms side-by-side, see our payroll software comparisons.
Quick answers for this use case.
