10 Best Payroll Software For Nonprofit Organizations in 2025

HR Industry Insights

7 minutes

September 29, 2025

Written by Hirex

Payroll for nonprofits? It's complicated. You must follow tax rules, stay transparent for donors, and align payroll with funding. It's like balancing on a moving rope! Let's explore 10 payroll systems nonprofit leaders use and love.

1. Rippling

Rippling takes the "all-in-one" approach seriously. This platform bundles payroll, HR, IT, and spending management into a single system - which is exactly what resource-stretched nonprofits need. No more juggling five different platforms just to pay your team and track their hours.

Rippling key features

Here's what makes Rippling stand out: payroll runs complete in just 90 seconds. That's faster than making coffee! ☕

The platform handles the compliance headaches automatically:

• Tax calculations, withholdings, and payments at every level - federal, state, and local

• All those W-2s, W-4s, and 1099s go completely paperless

• Garnishment support with optional payment handling

• Multiple pay rates and approval workflows for security

Rippling ideal nonprofit use case

Growing nonprofits managing staff across multiple locations will love Rippling's job code tracking. You can slice and dice hours by time, projects, location, and even specific grants. That's mission-critical for organizations juggling different funding sources.

The reporting capabilities really shine for transparency-focused nonprofits. You can trace every hour and dollar back to specific funding sources, making grant reporting much less painful.

2. Gusto

Gusto gets nonprofit payroll right: less time on admin, more on your mission. It simplifies payroll so much you might forget it's happening.

Gusto key features

Here's what makes Gusto stand out for nonprofit organizations:

• Full-Service Payroll Processing: Run unlimited payrolls for employees and contractors with automatic tax withholdings, direct deposit, and year-end forms. No surprises or extra fees.

• Time Tracking: Allow staff to log hours, categorize by project or grant, and submit weekly timecards—ideal for nonprofits with restricted funds; making grant reporting easier.

• Benefits Administration: Offer health, dental, vision, and life insurance nationwide; often difficult for small nonprofits.

• Compliance Support: Use built-in tools to stay audit-ready by tracking changing employment laws, giving peace of mind.

• QuickBooks Integration: Sync smoothly with QuickBooks and other accounting platforms for accurate payroll and bookkeeping data.

Gusto users save about 5 hours per month and $5,300 annually after switching from ADP, freeing up time and money for your programs.

Gusto ideal nonprofit use case

Gusto works perfectly for small to medium-sized nonprofits that want payroll to just work without the headaches. Here's where it really shines:

• Small education nonprofits with about 10 staff can save over 8 hours monthly on payroll and get better PTO insight.

• Community development nonprofits with around 20 employees benefit from Gusto's benefits management and QuickBooks integration.

• Volunteer-heavy nonprofits value Gusto's support for quick, compliant stipend and reimbursement payments.

One nonprofit leader said, "I'm a musician and arts nonprofit leader, initially unfamiliar with hiring, payroll, and filings. Gusto simplifies these tasks." Bottom line? For payroll software easy enough for non-IT professionals, Gusto is a great choice.

3. ADP

Been around since payroll was done by hand? That's ADP. With over 75 years, this veteran provider knows what nonprofits need to stay compliant and manage finances. Serving 13,000-15,000 nonprofits yearly, their track record is reassuring.

ADP key features

Here's what makes ADP stand out for mission-driven organizations:

• Secure electronic payments for staff and volunteers with multiple options.

• Automated tax management includes calculations, deposits, filings, and reconciliations.

• Grant tracking converts staffing data into funding.

• Integrates with QuickBooks, Peachtree, Xero, and other accounting platforms.

• Over 15 clear reports help analyze payroll and employee data.

Small nonprofit with under 50 staff? RUN Powered by ADP® is designed for you. Growing? ADP Workforce Now offers HR, benefits, and talent management.

ADP ideal nonprofit use case

ADP excels for established nonprofits like Operation PAR, a substance abuse treatment group that used ADP's real-time staffing data for grant success.

It benefits organizations with multiple locations by offering trend analysis, allowing strategic planning. Overall, ADP is ideal for nonprofits needing a payroll system that supports funding strategies and growth.

4. OnPay

OnPay truly understands nonprofits, unlike other payroll companies. They built their platform specifically for mission-driven groups, especially nonprofits and religious organizations needing tailored solutions.

OnPay key features

Here's what makes OnPay worth your attention:

• Unlimited payroll runs with automatic tax calculations, payments, and filings across all 50 states.

• Multiple payment options like direct deposit, debit cards, and self-printed checks at no extra cost.

• Employee portal for pay stubs and tax forms access. HR tools for onboarding, electronic signing, and PTO tracking.

• Benefits administration with major providers.

• Custom reporting with real-time data, downloads, and software integration.

OnPay even handles Form 943 filing for agricultural companies and manages local tax compliance - pretty handy if your nonprofit works in specialized sectors.

OnPay ideal nonprofit use case

OnPay suits small to medium nonprofits seeking simple payroll. It helps delegate tasks securely with six permission levels, allowing bookkeepers to run payroll without accessing sensitive data.

5. QuickBooks Payroll

Already using QuickBooks for your nonprofit? Good news: its payroll add-on could complete your financial setup. It seamlessly connects with your existing accounting, reducing data mismatches, easing your workload, and providing cleaner records for auditors.

QuickBooks Payroll key features

This system gets the job done with features that actually matter for nonprofits:

• Full-service payroll processing automatically handles calculations, filings, and taxes.

• Auto Payroll for salaried employees on direct deposit requires only review and approval.

• Payment options include next-day or same-day direct deposit.

• Tax forms like 1099-MISC and 1099-NEC can be filed and paid automatically.

• Employees access pay stubs, W-2s, and personal details through a self-service portal.

• HR services cover health insurance, 401(k), and workers' compensation.

What's nice is how it handles different pay structures - salaries, hourly wages, commissions, and bonuses. Perfect for nonprofits with mixed staffing arrangements.

QuickBooks Payroll ideal nonprofit use case

This solution suits small to mid-sized nonprofits using QuickBooks, offering a unified financial management system that simplifies reporting and fund tracking. For nonprofits with employees and contractors, QuickBooks Payroll handles diverse payment types and tax classifications with automation, saving time so your team can focus on your mission.

6. Square Payroll

Square Payroll offers hassle-free payroll, ideal for nonprofits already using Square for donations or retail. No learning curve or complex setup—just reliable payroll that gets the job done.

Square Payroll key features

Square keeps things simple with the essentials:

• Automated tax management with calculations, payments, and filings at federal and state levels.

• Flexible payment options include direct deposit, checks, or Cash App.

• Time tracking imports hours from Square POS or Square Team App.

• Unlimited payroll runs without extra fees.

• Employee self-service allows staff to access pay stubs and tax documents independently.

Want benefits? They've got partnerships for health insurance, retirement plans, and workers' compensation. Nothing fancy, but it covers what most small nonprofits need.

Square Payroll ideal nonprofit use case

This one's easy. Square Payroll suits small nonprofits in the Square ecosystem. It handles both employees and contractors effortlessly. Need basic payroll without HR extras? It's a perfect fit.

7. Patriot Payroll

Patriot Payroll offers a straightforward, reliable solution for nonprofits with tight budgets. It avoids unnecessary features, focusing on essential payroll processing without extra costs.

Patriot Payroll key features:

Patriot keeps things refreshingly simple with their three-step payroll process:

• Enter hours (manually or through time tracking integration)

• Review automatic calculations

• Approve with one click and distribute payments

That's it. No complicated workflows or confusing menus. The essentials are covered: unlimited payroll runs, free direct deposit, employee self-service portals, and automatic tax calculations. Employees and contractors are paid through the same system, and you can track expenses by department for grant reporting.

Perfect Fit for These Nonprofits

Patriot suits small nonprofits under 50 employees needing simple payroll. If your focus is on accurate, affordable payroll over extra features, Patriot is ideal.

The system handles nonprofit payroll requirements while letting you focus your limited resources on what actually matters - your mission. Sometimes simple really is better.

8. Justworks

Here's the deal with Justworks: it's a PEO, acting as your co-employer. While complex, this setup allows small nonprofits to access benefits like larger firms. When was the last time your 15-person nonprofit matched Google on health insurance?

Justworks key features

Justworks handles the full spectrum of what nonprofits need to keep their teams happy and compliant:

• Multi-state payroll handles different pay rates and contractor payments effortlessly.

• Compliance management covers tax filings, W-2s, 1099s, and unemployment forms.

• Team tools include simple onboarding, PTO tracking, and accounting integrations.

• Support available 24/7 via phone, chat, or help center.

• Enterprise benefits like medical, dental, vision, 401(k), and HSA/FSA at small-team rates.

Justworks ideal nonprofit use case

Justworks suits small to medium nonprofits with 5-30 employees across states. It simplifies HR, offers attractive benefits, and manages multi-state compliance, earning praise for handling complex laws. If benefits matter and you want to attract top talent, it might be worth the cost.

9. Remote

Remote work has transformed nonprofit team-building, growing 140% since 2005, as organizations adapt to increasingly distributed teams. Your payroll system must handle this complexity.

Remote key features

Remote payroll solutions give nonprofits some serious advantages they didn't have before:

• Multi-state compliance management that actually knows the tax rules in Ohio are different from California (and handles both without you losing sleep)

• Flexible payment options supporting international and domestic payments in local currencies

• Consolidated HR functions including streamlined onboarding, document management, and time tracking

• Enhanced security protocols protecting sensitive payroll data for dispersed teams

• Automated tax filings across multiple states where employees may reside

Remote ideal nonprofit use case

Remote payroll solutions suit nonprofits ready to hire beyond their zip codes, especially during rapid growth. Hybrid nonprofits, where the development team is remote, but service staff are onsite, benefit from systems that handle diverse workforce setups, avoiding rigid payroll structures.

10. Zoho Payroll

Zoho Payroll integrates well with other Zoho tools, making it ideal if you're already in their ecosystem. With 25+ years of experience, they develop simple systems suited for resource-limited nonprofits.

Zoho Payroll key features

• Multi-state compliance that actually works when your team is scattered across different states

• Flexible payment schedules because not everyone needs to be paid the same way - 2-day or 4-day direct deposit options

• Custom user roles so you can delegate without losing sleep over security

• Employee self-service portal where your staff can grab their paystubs and tax docs whenever they need them

• Automatic tax calculations handling federal, state, and local requirements without the headaches

• Integration magic connecting with Zoho Books for accounting and Zoho Expense for reimbursements

Zoho Payroll ideal nonprofit use case

Zoho Payroll excels if you're in the Zoho ecosystem. Manages multi-state employees with compliance features. Offers 100+ reports for insights on labor costs and trends. Ideal for nonprofits automating routines while controlling budgets.

Final Words 🎤

Choosing your nonprofit's payroll system is a crucial decision that saves time and lets you focus on your mission. We've reviewed 10 options. Budget-friendly choices like Square and Patriot cover essentials, while Justworks provides big-company benefits for smaller nonprofits.

The right system automates compliance, processes payments smoothly, and provides necessary reports. Don't overthink; choose a system that fits your current needs and budget. Most providers offer trials or demos. Let technology handle payroll so you can focus on your mission.