Payroll Services
Best Payroll Services for Nonprofits
Nonprofit payroll has to pay staff correctly and show which program or grant each paycheck belongs to. A payroll service should split labor cost by funding source, feed the accounting system, keep volunteers off payroll, and price clearly enough to fit a grant budget.
- products that fit
- 6
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Top 4 by LeadChange Scoreof 6 that fit · 2 not scored yet · scored for nonprofits (reweighted)
OnPay6.9 out of 10, Medium confidence
Paychex Flex6.2 out of 10, Medium confidence
Paycor6.1 out of 10, Medium confidence
Netchex4.8 out of 10, Medium confidence
Patriot PayrollNot scored yet
Vensure Employer SolutionsNot scored yet
See the full rankingMedium confidence
Payroll services 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
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 employee3
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.
Netchex
Netchex suits US employers with hourly, frontline teams, such as restaurants, hotels, clinics, retailers and manufacturers, that want payroll, tax filing, time, HR and benefits in one cloud system with an assigned implementation lead.
- Pricing model
- Quote only6
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.
Not scored yetFrom $37/mo + $5/employee/mo (Full Service Payroll plan)7
Patriot Payroll plans and prices
Show all 6 products
- Vensure Employer SolutionsNot scored yet (12 of 24 facts verified)What Vensure Employer Solutions costs
LeadChange Score: editorial assessment based on public information.
What matters for nonprofits
Time by grant
Charges to federal awards for salaries and wages must be based on records that accurately reflect the work performed. Ask how time is coded by grant and how it reaches the general ledger.
Exempt-organization taxes
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 provider sets up your exemption correctly.
Volunteers kept off payroll
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. Make sure the line is clear before anyone is added.
Clear pricing for a grant budget
Budgets are set in advance. Ask for the full monthly price at your headcount, including year-end forms and each extra state.
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
Find your fit
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- All payroll services, ranked
The full ranking, top picks and how to choose.
- Payroll Services comparison table
Every product side by side: score, price and verified features.
- Payroll Services pricing guide
Published list prices, cost by headcount and fees to ask about.
- Payroll services for small business
The ranking reweighted for small business.
- Payroll services for mid-sized companies
The ranking reweighted for mid-sized companies.
- Payroll services for healthcare
The ranking reweighted for healthcare.
- Payroll services for manufacturing
The ranking reweighted for manufacturing.
Frequently asked questions
Do nonprofits pay payroll taxes?
Yes. The IRS says a tax-exempt organization with employees is responsible for federal income tax withholding and for Social Security and Medicare taxes, and some exempt organizations are also responsible for federal unemployment tax. A payroll service should set up the organization's exemption status so it files and pays only the taxes that apply.
What should a payroll service for nonprofits include?
Payroll costs split by grant, program or fund, journal entries in the format of your accounting system, the right tax setup for an exempt organization, and a clear monthly price you can put in a grant budget. Ask for a sample report that splits one pay run by funding source.
Which payroll services for nonprofits offer a free trial?
OnPay and Patriot Payroll list a free trial, according to their vendors: 2 of the 6 products for nonprofits.
Which payroll services for nonprofits have SOC 2 Type II?
OnPay, Patriot Payroll, and Paycor state SOC 2 Type II compliance. That is 3 of the 6 products for nonprofits.
Which payroll services for nonprofits integrate with QuickBooks Online?
QuickBooks Online, listed by 3 of the 6 payroll services for nonprofits: Netchex, OnPay, and Patriot Payroll.
Which payroll services for nonprofits have a mobile app?
Netchex, Patriot Payroll, Paychex Flex, Paycor, and Vensure Employer Solutions confirm a mobile app; 1 of the 6 products for nonprofits does not document one.
Which payroll services for nonprofits are built for enterprises?
Netchex and Paycor list enterprises among the company sizes they serve.
How we research
This ranking of payroll services 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
19 verified facts, each checked against the vendor's own pages or another primary source, most recently on Oct 22, 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
Who pays us never changes a score or a rank. If something here is wrong, tell us and we correct it publicly. Request a correction
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Sources
The 8 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
- OnPay onpay.com/payroll/software/costs-pricing“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.”
- Netchex netchex.com/netchex-faqs“Netchex charges per-employee, per-month (PEPM), not per payroll. Netchex utilizes quote-based pricing, which can vary depending on the size of your company and the services you are interested in.”
- Patriot Software patriotsoftware.com/pricing“Basic Payroll is $17/month + $4 per worker paid; Full Service Payroll is $37/month + $5 per worker paid.” “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.”