Payroll Software
Best Payroll Software for Nonprofits
Nonprofit payroll pays staff and also shows which program or grant each paycheck belongs to. The right software codes wages by funding source, sends them to fund accounting, handles the taxes an exempt organization owes, and keeps volunteers off payroll.
- products that fit
- 9
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Top 6 by LeadChange Scoreof 9 that fit · 2 not scored yet · scored for nonprofits (reweighted)
OnPay7.9 out of 10, Medium confidence
Paychex Flex7.3 out of 10, Medium confidence
Paycor6.9 out of 10, Medium confidence
Rippling6.2 out of 10, High confidence
Paylocity6.1 out of 10, Medium confidence
Netchex5.6 out of 10, Medium confidence
Workday HCMNot scored yet
NamelyNot scored yet
See all 9 rankedHighMedium confidence
Payroll software for nonprofits, ranked
Ranked by LeadChange Score from verified facts; products with too few verified facts are not scored yet and come last. Prices are list prices as published by each vendor.
Filter by verified facts
Patriot Payroll
Patriot Payroll suits small US employers that want simple, inexpensive payroll with published prices and US-based support. Basic Payroll is $17 a month plus $4 per worker paid, and Full Service, which files federal, state and local taxes, is $37 plus $5 per worker. Payroll runs, direct deposit and setup help are free.
OnPay
OnPay suits US small businesses that want full-service payroll at one published price: $49 a month plus $6 per worker, with federal, state and local tax filings, W-2s, 1099s, multi-state payroll and unlimited pay runs included. Setup and data migration are free, and support is by phone, chat and email.
Paychex Flex
Paychex Flex suits US small and mid-sized employers that want unlimited payroll runs, automated multi-state tax filing and room to add HR, time tracking and benefits from one vendor. Paychex was founded in 1971 and is a public company.
- Pricing model
- Base fee + per employee5
Paycor
Paycor suits US employers from small businesses to companies with 1,000+ employees that want payroll, HR, time, recruiting and talent tools on one platform with open APIs. Plans run from Basic payroll to Complete + ASO, all priced by quote. It holds SOC 1 and SOC 2 Type 2 attestations and supports single sign-on.
Rippling
Primarily HRIS software; payroll module is secondary
Rippling suits companies that want HR, payroll, IT and finance on one employee database and are ready to buy each product separately. Payroll for small businesses starts at $8 per user per month plus a $40 base fee.
Show all 9 products
- Paylocity6.1/10 · Medium confidenceWhat Paylocity costs
- Netchex5.6/10 · Medium confidenceNetchex pricing
- Workday HCMNot scored yet (13 of 26 facts verified)Workday HCM pricing
- NamelyNot scored yet (12 of 26 facts verified)Namely plans and prices
LeadChange Score: editorial assessment based on public information.
What matters for nonprofits
Wages coded by grant
Charges to federal awards for salaries and wages must be based on records that accurately reflect the work performed. Check that every pay line carries a fund, program or grant code.
Fund accounting sync
Journal entries should arrive in the accounting system with those codes, so no one re-allocates payroll by hand each month.
Taxes for exempt organizations
A tax-exempt organization with employees withholds income tax and pays Social Security and Medicare taxes; only some exempt organizations owe federal unemployment tax. Check that the software lets you set your exemption.
Volunteers and contractors kept apart
Volunteers for charitable purposes are not employees under federal wage law, but paid staff cannot volunteer for the same type of work they are paid to do. Keep each group in its own record.
More tools for nonprofits
- 401(k) Providers401(k) providers for nonprofits
- Applicant Tracking SystemsApplicant tracking systems for nonprofits
- ASO ServicesASO services for nonprofits
- Background Check ServicesBackground check services for nonprofits
- Benefits AdministrationBenefits administration for nonprofits
- COBRA AdministrationCOBRA administration for nonprofits
- Employee Engagement SoftwareEmployee engagement software for nonprofits
- Employee Scheduling SoftwareEmployee scheduling software for nonprofits
- HRIS SoftwareHRIS software for nonprofits
- Onboarding SoftwareOnboarding software for nonprofits
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- Payroll Software pricing guide
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- Payroll software for small business
The ranking reweighted for small business.
- Payroll software for mid-sized companies
The ranking reweighted for mid-sized companies.
- Payroll software for retail
The ranking reweighted for retail.
- Payroll software for healthcare
The ranking reweighted for healthcare.
Frequently asked questions
How do nonprofits allocate payroll costs to grants?
By recording time by grant, program or fund and charging wages in proportion. Under federal grant rules, charges to federal awards for salaries and wages must be based on records that accurately reflect the work performed. Payroll software should carry a funding code on each pay line and send it to fund accounting with the journal entry.
What should payroll software for nonprofits include?
Wages coded by grant or fund, a connection to the fund accounting system, a tax setup for an exempt organization, and separate records for volunteers and contractors. Ask the vendor to show one pay run split across two grants.
Can nonprofits have a payroll?
Yes. A nonprofit that pays people for their work runs payroll like any employer. The IRS says every exempt organization with employees withholds income tax and pays Social Security and Medicare taxes, while only some also owe federal unemployment tax, so set the exemption in the payroll software. Volunteers who give their time for charitable purposes are not paid through payroll.
Can nonprofits get a payroll tax credit for hiring veterans?
Yes. Under the work opportunity tax credit, qualified tax-exempt organizations that hire eligible unemployed veterans may be able to claim the credit against their payroll tax liability, using Form 5884-C, according to IRS Publication 15. Ask a payroll provider whether it prepares that form with your quarterly filings or leaves it to you.
What is the 33% rule for nonprofits?
It usually means the IRS public support test: a charity qualifies as publicly supported if it normally receives at least one-third of its total support from government units, from contributions by the general public, or from a combination of these, according to IRS Publication 557. The test looks at where support comes from; it does not limit what a nonprofit pays in wages.
What is the best payroll software for nonprofits?
On the LeadChange Score weighted for nonprofits, the highest-scoring of the 7 products with a published score are Patriot Payroll (9.1/10), OnPay (7.9), and Paychex Flex (7.3).
Which payroll platforms for nonprofits have SOC 2 Type II?
OnPay, Patriot Payroll, Paycor, Paylocity, Rippling, and Workday HCM state SOC 2 Type II compliance; Paylocity, Rippling, and Workday HCM also hold ISO 27001. That is 6 of the 9 products for nonprofits.
Which payroll platforms for nonprofits integrate with QuickBooks Online?
QuickBooks Online, listed by 3 of the 9 payroll platforms for nonprofits: Netchex, OnPay, and Patriot Payroll.
Which payroll platforms for nonprofits have a mobile app?
Namely, Netchex, Patriot Payroll, Paychex Flex, Paycor, and 3 more confirm a mobile app; 1 of the 9 products for nonprofits does not document one.
Which payroll platforms for nonprofits are built for enterprises?
Netchex, Paycor, Paylocity, Rippling, and Workday HCM list enterprises among the company sizes they serve.
How we research
This ranking of payroll software for nonprofits reweights the LeadChange Score: capability coverage 35%, pricing transparency & value 15%, integrations & API 10%, security & compliance 15%, fit & support 15%, and data confidence 10%. Only products with a verified fact showing they serve this segment are listed.
How this page was made
What it is built from
43 verified facts, each checked against the vendor's own pages or another primary source, most recently on Oct 24, 2026.
Method
Scored and compared with the LeadChange methodology, version 1.3. Read the methodology
Independent review
Our independent review of Oct 28, 2026 asked for changes. How we review
Hands-on testing
We have not tested these products hands-on: this page uses public information only.
Who made it
The LeadChange Research Team, following a written research process. No named expert has reviewed this page. About us
Independence and errors
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Sources
The 10 pages this page's facts come from, with the day we last checked each one. The numbers beside the figures above link here.
Quotes from the sources
- Patriot Software patriotsoftware.com/pricing“If you use Patriot’s payroll software, you will be charged $4 (Basic) or $5 (Full Service) per worker you pay during the month.” “Our payroll is a flat monthly fee + per worker paid fee. Run as many payrolls as you need. We'll bill you in arrears each month.”
- Patriot Software patriotsoftware.com/about“As a SOC 2 Type II compliant organization, we follow rigorous data protection standards and adhere to all required federal privacy, anti-fraud, and security regulations.”
- OnPay onpay.com/payroll/software/costs-pricing“Payroll Essentials $49 base + $6/worker per month” “Get started at just $49 base + $6/worker per month. No hidden fees, ever.”
- OnPay onpay.com/security“Third-party Certification: OnPay holds third-party auditor certification with the AICPA’s SOC program and is SOC 2 Type II compliant.”
- Paychex paychex.com/payroll/paychex-flex-essentials“Our most affordable option: Only $39/mo. + $5 per employee”
- Paycor paycor.com/plans-pricing“Answer a few questions to get a custom price quote if you're a small business or view our mid-market product plans.”
- Paycor paycor.com/compliance-solutions/security“Paycor is accredited by and compliant with GDPR, FinCEN, US Privacy Shield, SOC 1 Type 2, and SOC 2 Type 2 security standards.”
- Rippling rippling.com/solutions/small-businesses“Rippling's small business plans start at $8 per user per month for payroll. The final cost depends on which other products you add, such as benefits administration, time and attendance, or IT device management.”
- Rippling rippling.com/pricing“While most Rippling products are billed on a simple per-employee, per-month basis, some may be charged at (or include) a monthly basis fee.”
- Rippling rippling.com/trust/security“Rippling's SOC 2 Type 2 report covers the trust services categories of Security, Confidentiality, and Availability, and is audited annually.”