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 $49/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 | $49/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.
How each pick fits nonprofits: what to validate in a trial, with links to our full reviews and official sites.
Gusto is approachable payroll software for nonprofits that pay modest W-2 program staff and 1099 facilitators, trainers, or grant consultants from one modern platform. Transparent pricing helps lean teams adopt full-service payroll without a lengthy vendor committee. During your first payrolls, confirm deposits, any stipend or housing allowance treatments your board approved, and clear separation between employee wages and independent contractor payouts for audit trails. Run a test month with split allocations across two programs if you track functional expense, plus a 1099 speaker honorarium, to see dimensions survive export. If you use departments for admin versus mission, verify payroll detail before the finance committee packet. Scale benefits when you hire a second full-time coordinator.
QuickBooks Payroll is payroll software nonprofits choose when QuickBooks already tracks funds, grants, and classes, and they need labor posted for reimbursement-ready grant reporting. Program versus management splits depend on payroll landing in the same class structure auditors expect. On trial payrolls, reconcile payroll to at least two grants or programs and confirm salary allocations, fringes, and employer taxes map correctly before you file reimbursement requests. Integrate QuickBooks Time if hourly staff log hours by grant line. Validate multi-state rules if remote workers live outside your incorporation state. Clean allocations reduce pain during single audits and foundation reviews.
OnPay is payroll software for nonprofits that want flat, predictable pricing while boards scrutinize every administrative dollar. Support helps when a fiscal sponsor transition or new grant suddenly changes how you classify contractors. Use early payrolls to prove deposits, new-hire reporting, and 1099 workflows for recurring teaching artists or evaluators. Import a payroll with split allocations, PTO payouts, and stipends to confirm taxable versus non-taxable treatment matches policy and donor restrictions. Map GL exports once so fund balances stay tied out after each close. Predictable fees help when donations arrive quarterly but payroll is biweekly.
ADP is payroll software to evaluate for larger nonprofits, affiliates, or multisite human-services organizations that need serviced payroll, deeper HR, and multi-state compliance as they scale. Quoted implementations align earning codes with how you report functional expenses to the IRS and major funders. After go-live, audit tax registrations for every state where remote staff work, not just headquarters. Test inter-entity payroll if chapters or subsidiaries share services. If unionized staff or complex fringe benefits appear, review deductions and reporting with ADP during the first quarter. Compare serviced cost to mid-market peers once those controls prove out.
Head-to-head comparisons to narrow your choice.
Gusto and QuickBooks Payroll both handle W-2 and 1099 payroll with automatic tax filing, but they target different workflows. Gusto is a sta…
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Compare →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.
