The Best Payroll Software for Nonprofits for 2024: Compared

Managing payroll for nonprofit organizations involves juggling priorities from optimizing costs to paying accurate wages and taxes. However, nonprofits often lack the time and expertise to perform payroll manually. That’s where payroll software comes in.

ADP is our pick for the best overall payroll software for nonprofits. It offers essential features like automated payroll and tax filing, benefits administration, and compliance tools, covering mission-focused nonprofits from all angles.

However, each nonprofit is different. Below, we review 7 leading platforms so you can find the right fit, whether you’re looking for payroll software as a small organization or a global nonprofit.

The Best Payroll Software for Nonprofits Ranked

  • ADP: Best overall payroll for nonprofits
  • Deel: Best for global nonprofits
  • Patriot Software: Best for affordability
  • Rippling: Best for customizing and automating payroll
  • QuickBooks: Best for integrating with QuickBooks Bookkeeping
  • Gusto: Best for generous essentials plan
  • OnPay: Best for straightforward pricing

The Best Payroll Software for Nonprofits Reviewed

We ranked our top payroll software for nonprofit organizations based on factors including affordable pricing, ease of use, third-party integrations, key features like automated payroll and tax filing, and premium features like project and time tracking.

ADP – Best overall payroll for nonprofits

Screenshot of ADP payroll dashboard including a search bar, a to-do list, and a bar chart with payroll figures.

Starting Price Free Trial Top Features Countries Covered Reporting
Book a demo to get a custom price ✅(3 or 4 months) • Streamlined payroll and tax filing
• Recruiting tools
• Comprehensive HR add-on modules
140+

ADP offers all-in-one payroll functionality for nonprofits of all sizes in the US and abroad. It includes automated payroll, tax filing, and payment, employee self-service, a free employee debit card, 24/7 support, and 700+ integrations with third-party apps, including accounting and collaboration. The job costing feature helps nonprofits track labor costs against funding streams.

Higher-tier plans let you post jobs on ZipRecruiter and streamline job description creation. For an extra cost, you can add other useful ADP modules, including time tracking, workforce management, and hiring.

ADP vs. Deel

Deel and ADP both suit global nonprofits with automated payroll and tax filing, onboarding, compliance tools, and background checks.

While Deel’s plans include leave and benefits management, on ADP, you add them for an extra cost. Deel also lets you hire through an EOR where you don’t have entities globally and handles immigration tasks for you. However, you might go for ADP for comprehensive add-on modules, including time tracking and hiring.

ADP vs. Gusto

Both Gusto and ADP provide streamlined payroll, tax filing, employee onboarding, hiring tools, time tracking, and customizable reporting.

However, Gusto features project and time tracking, benefits administration, PTO management, performance reviews, employee surveys, and hiring tools in one competitively-priced plan— on ADP, you only access these features by combining several standalone modules. That said, ADP suits nonprofits preferring a fully hands-off HR experience with AI-driven automation.

Read the full ADP review.

ADP Pricing Plans

  • Essential: Automated multi-jurisdiction payroll, tax filing, Wisely Direct debit cards for employees, onboarding, background checks, employee portal, and employee discounts
  • Enhanced: Everything on Essential plus labor law poster compliance, job costing, and ZipRecruiter job posting
  • Complete: Everything on Enhanced plus HR helpdesk, salary benchmarks, and HR training and toolkits
  • HR Pro: Everything on Complete plus enhanced HR helpdesk, applicant tracking system, and learning management system

ADP offers custom pricing when you schedule a product demo. You get a 3 or 4-month free trial, depending on your business size and plan. This is the most generous trial on our list.

Pros

  • One-stop-shop payroll solution
  • Useful workforce analytics
  • Large number of integrations
  • Highly customizable
  • Suitable for global workforce

Cons

  • Learning curve for beginner HR staff
  • Benefits and PTO management charged separately
  • Can get pricey with add-ons

Deel – Best for global nonprofits

A Deel software window containing a list of employees and contractors, their country, and their upcoming payment figures.

Starting Price Free Trial Top Features Countries Covered Reporting
$49/month for contractors • Global payroll
• Immigration support
• Time off & expense management
150+

Deel’s payroll platform ticks all the main boxes, offering payroll and tax filing automation, an employee portal, compliance tools, and key third-party integrations.

It stands out for its global hiring services, including Employer of Record (EOR) hiring, where you don’t have entities, immigration support, and background checks. Plus, HR features, including time off, benefits, and expense management, are free for up to 200 people—excellent news for budget-conscious nonprofits.

Deel vs. Gusto

Both Deel and Gusto offer automated payroll benefits management, including 401(k), paid time off (PTO), and document management.

Gusto additionally offers an employee time clock that helps streamline timesheet approval and payroll. However, Deel lets you easily hire employees outside the US, access visa support, and run background checks.

Deel vs. QuickBooks

QuickBooks and Deel both help you manage payroll, benefits, tax filing, and time off with 24/7 customer support. While both offer comprehensive compliance tools, QuickBooks additionally offers labor law posting support, covering you for up to $33,000 in related fines.

Plus, QuickBooks Payroll integrates seamlessly with other QuickBooks products like bookkeeping and time tracking. You might still pick Deel for its global hiring service, background checks, and free HR module (up to 200 users).

Read the full Deel review.

Deel Pricing Plans

  • Deel HR (Free up to 200 employees): HR admin and reporting only, without payroll
  • Contractors (starts at $49/month): International payroll for contractors
  • Global Payroll (custom quote): Multi-country payroll where you have entities
  • EOR (starts at $599/month): Multi-country hire and payroll where you don’t have entities

You must contact Deel for a Global Payroll plan quote. However, its contractor-only payroll plan is slightly above competitor equivalents like Gusto’s (starting at $35 + $6/user/month). For nonprofits with 200 employees or less, getting free HR features is unrivaled on our list.

Pros

  • Simple global hiring
  • Immigration support and background checks
  • Includes benefit administration
  • Free HR tools for up to 200 users

Cons

  • No time tracking
  • No free trial
  • No grant or project tracking

Patriot Software – Best for affordability

A Patriot Software payroll window titled Tax Filings containing a W-2 confirmation, quarterly forms, and a button titled Run Report.

Starting Price Free Trial Top Features Countries Covered Reporting
$17/month + $4/employee/month ✅(30 days) • Quick payroll and tax filing
• Employee portal
• Report labor costs by department
1 (USA)

For cost-conscious nonprofits with in-house HR and payroll experts, Patriot Software is a top choice. It covers the basics, including customizable payroll, time off accruals, tax filing and payment, an employee portal, and cost reports customizable by department. For a reasonable extra cost, you can throw in a time tracking or HR module.

Patriot Software vs. QuickBooks

Both QuickBooks and Patriot Software offer unlimited payroll runs, tax filing, employee self-service, optional time tracking, and accounting software integrations.

Unlike Patriot, however, QuickBooks lets you automate payroll, manage benefits in-app, and submit next-day direct deposits—which could enhance your employees’ experience. You might still choose Patriot Software because adding time tracking to its plans is overall cheaper than the QuickBooks Premium plan featuring a time clock.

Patriot Software vs. ADP

Patriot and ADP address different nonprofit needs, though they both offer basic payroll, tax filing, and time-tracking tools.

ADP is better suited to large or international nonprofits needing an all-in-one HR platform that also includes hiring, onboarding, performance reviews, and workforce management. Meanwhile, Patriot is super cost-effective for smaller nonprofits that can perform compliance tracking, onboarding, hiring, and benefits administration in-house.

Read the full Patriot Software review.

Patriot Software Pricing Plans

  • Basic payroll ($17/month + $4/employee/month): Pay employees and contractors, handle your own payroll taxes
  • Full-service payroll ($37/month + $4/employee/month): Pay employees and contractors, let Patriot handle payroll taxes
  • HR add-on ($6/month + $2/employee/month): Store, manage, and report on employee data
  • Time and attendance add-on ($6/month + $2/employee/month): Let employees clock in, view time off, manage overtime rules

Patriot Software’s basic plan offers the best value on our list if you want to pay your own taxes. The full-service plan is also extremely affordable, say, compared with Gusto’s cheapest plan for instance (starting at $40/month + $6/user/month). However, you could incur significant charges for additional state payroll tax filings, costing $12/month/state.

Pros

  • Great value for cash-strapped nonprofits
  • Reports customizable by location and department
  • Time tracking add-on for a low price
  • Guaranteed tax filing accuracy
  • Free 30-day trial

Cons

  • No benefit, time off, or compliance tracking
  • No automated payroll
  • No international payroll
  • Additional state filings cost $12/month/state

Rippling – Best for customizing and automating payroll

A screenshot of the Rippling payroll dashboard, including a search bar, upcoming tasks, and buttons to Rippling apps, including benefits, time and attendance, and recruiting.

Starting Price Free Trial Top Features Countries Covered Reporting
$8/user/month • Grant tracking payroll reports
• Automated compliance checks
• Workflow automation
+145

Rippling is terrific for scaling nonprofits with advanced payroll customization needs. Its payroll platform includes time off tracking, US and international tax filing, reports customizable by grants and job codes, and workflow automations such as compliance checks. You can easily add extra HR modules, including recruiting, learning management, and employee surveys.

Rippling vs. OnPay

Rippling and OnPay both offer full-service payroll and automated tax filing, PTO tracking, and benefits administration.

You might pick OnPay for its simple, affordable single plan that includes expert support—however, it wouldn’t serve growing nonprofits as well as Rippling, which offers 500+ integrations, time-saving workflow automations, and customizable reports. Furthermore, Rippling lets you add extra HR modules as needed, including hiring and learning management.

Rippling vs. ADP

Both Rippling and ADP suit scaling nonprofits. They let you stack extra HR modules on top of essential payroll features, from recruiting and onboarding to performance reviews and employee surveys. Both platforms integrate with an impressive 500+ third-party apps—helping nonprofits be more efficient and save time.

Compared with ADP, Rippling boasts more advanced customization and automation options. However, you might need tech-savvy in-house staff to customize and use the platform effectively. Meanwhile, you might choose ADP for its highly-rated customer support, hands-on compliance support, and HR outsourcing services.

Read the full Rippling review.

Rippling Pricing Plans

Rippling Unity is the base workforce management platform, starting at $8/user/month.

  • Core: Store, track, report on employee data, and automate workflows
  • Pro: Everything on Core plus 10 custom workflows, formula fields, and advanced reports
  • Unlimited: Everything on Pro plus webhooks and unlimited workflows, formula fields, and advanced reports

Each additional module, including payroll, is priced separately. You need to contact Rippling to get a custom quote.

Pros

  • Advanced customization and automation options
  • Filter reports by grants and projects
  • Automated compliance checks and alerts
  • Optional HR modules including hiring and surveys
  • Suitable for growing global nonprofits

Cons

  • No free trial
  • Steep learning curve
  • May require tech-savvy staff

QuickBooks – Best for integrating with QuickBooks Bookkeeping

A screenshot of QuickBooks Payroll showing a payroll run form, including pay period, total pay, and a list of employees with their pay methods and regular, overtime, and sick hours.

Starting Price Free Trial Top Features Countries Covered Reporting
$45/month + $6/employee/month ✅(30 days) • Full-service payroll
• Benefits administration
• Time tracking
1 (USA)

QuickBooks is an affordable payroll choice for nonprofits, particularly when bundled with other QuickBooks products like bookkeeping or accounting. The Payroll plan alone offers auto-payroll, tax filing and payments, time tracking, and benefits administration. Higher-tier plans include project tracking, a personal HR advisor, and tax penalty protection.

Bundling with the bookkeeping module lets you track inventories and profitability, bill suppliers, and generate contractor invoices—offering an easy and affordable way to track multiple nonprofit cost streams.

QuickBooks vs. ADP

Both QuickBooks and ADP offer auto-payroll, benefits management, and compliance tools with 24/7 expert support.

However, ADP additionally offers add-on talent management and hiring modules—useful for nonprofits that need one platform for all employee management needs. You might choose QuickBooks, though, for its simple plans with built-in time tracking versus ADP’s extra time and attendance fees.

QuickBooks vs. OnPay

OnPay and QuickBooks both offer essential payroll tools in budget-friendly plans. They include tax filing and payment, benefit administration, and employee self-service.

OnPay, however, has just one all-inclusive plan, suiting nonprofits that require a clear, uncomplicated payroll solution. Unlike QuickBooks, OnPay also features PTO management. However, you might still prefer QuickBooks for its time and compliance tracking and seamless integration with QuickBooks Bookkeeping.

Read the full QuickBooks Payroll review.

QuickBooks Pricing Plans

  • Payroll Core ($45/month + $6/employee/month): Full-service payroll, employee portal, benefits administration, expert support
  • Payroll Premium ($80/month + $8/employee/month): Everything on Core plus time tracking, 24/7 support, and expert review
  • Payroll Elite ($125/month + $10/employee/month): Everything on Premium plus expert setup, project tracking, personal HR advisor, tax penalty protection

QuickBooks offers 50% off the base price for the first 3 months. Its pricing is only a pinch higher than the lowest-cost providers’. By comparison, OnPay’s all-inclusive plan and Gusto’s cheapest plan each cost $40/month + $6/user/month.

Pros

  • 30-day trial available
  • Includes on-the-go time and project tracker
  • Includes next-day direct deposits
  • Simple and cheap to integrate with other QuickBooks modules
  • Comprehensive compliance tools

Cons

  • No leave management
  • No HR add-on options such as hiring
  • Tax penalty protection only on the Elite plan

Gusto – Best for generous essentials plan

Illustrations of Gusto dashboards on a laptop and smartphone side by side.

Starting Price Free Trial Top Features Countries Covered Reporting
$40/month + $6/user/month • Full-service auto-payroll
• Time and project tracking
• Hiring and onboarding tools
75+

Gusto is an excellent choice for nonprofits requiring a cost-effective, easy-to-use payroll platform that covers all the bases. It includes automated payroll in all 50 states, tax filing and payments, employee self-service, time tracking, benefits management, and reporting. Plus, basic tools for onboarding, hiring, performance reviews, and surveys are baked into its plans.

Gusto vs. Rippling

Rippling and Gusto are both comprehensive payroll platforms providing automated payroll and tax filing, compliance tools, expense and benefits management, plus time tracking, performance management, surveys, and hiring tools.

That said, Rippling integrates with 500+ apps, and its features—reporting, in particular—are more customizable than Gusto’s. So, Rippling suits nonprofits with complex cost reporting or payroll customizations. However, learning to use Rippling may require staff time and expertise.

You might prefer Gusto’s intuitive interface and quick setup, plus its combination of essential tools in one plan, versus Rippling’s multi-module structure.

Gusto vs. Patriot Software

Both Gusto and Patriot Software offer affordable, user-friendly payroll tools, including employee self-service, tax filing and payment, reporting, and benefits management.

However, Patriot Software charges extra per additional state filing and doesn’t include Gusto features like auto-payroll, benefits and time off management, and time and project tracking. Additionally, Gusto offers hiring, onboarding, and performance review tools. Patriot is cheaper, though, and suits smaller nonprofits with in-house payroll experts.

Read the full Gusto review.

Gusto Pricing Plans

  • Simple ($40/month + $6/user/month): Single-state payroll, employee accounts and self-service, basic hiring and onboarding, benefits administration, reports
  • Plus ($80/month + $12/user/month): Everything on Simple plus Multi-state payroll, next-day direct deposits, advanced hiring and onboarding, time and project tracking, workforce costing, performance reviews, employee surveys
  • Premium (custom pricing): Everything on Plus plus dedicated customer success manager, compliance alerts, payroll migration, priority support, R&D tax credit discount
  • Contractor-only ($35 + $6/user/month): Unlimited payments across all 50 states, 4-day direct deposit

Gusto offers 25% off the first 3 months on the Plus plan. While there’s no free trial, Gusto’s plans are generously priced compared with alternatives. Patriot Software’s higher-tier plan is $37/month + $4/user/month but doesn’t include benefits administration, auto-payroll, or hiring and onboarding tools.

Pros

  • Comprehensive and affordable plans
  • Includes benefits administration
  • Includes time and project tracking
  • Includes hiring and onboarding tools

Cons

  • No free trial
  • Reports not as customizable as other competitors
  • Limited global payroll tools

OnPay – Best for straightforward pricing

Screenshot of an OnPay report page featuring several charts, including an employee count and wages bar chart and a pay types pie chart.

Starting Price Free Trial Top Features Countries Covered Reporting
$40/month + $6/user/month ✅(30 days) • Auto tax payments
• PTO tracking
• Payroll task delegation
1 (USA)

OnPay is a straightforward payroll software for nonprofits, helping you pay wages and taxes accurately, manage benefits, and stay compliant with just one affordable plan.

It handles multiple pay rates and overtime in all 50 states, automates taxes while managing 501(c)(3) exemptions, plus you get free account setup and expert support. In addition, admins can delegate internal payroll tasks to users—a handy feature.

OnPay vs. Patriot Software

Patriot Software and OnPay both offer payroll essentials, including unlimited payroll runs, an employee portal, time off accruals, and reporting.

Patriot Software’s higher-tier plan is cheaper overall than OnPay’s all-inclusive plan, but Patriot charges for each additional state filing. You might also choose Patriot because its reports are customizable by department and location. On the flip side, OnPay includes PTO management and benefits administration features.

OnPay vs. Deel

OnPay and Deel share core features like unlimited employee and contractor payrolls, tax filing and payments, PTO and benefits management, onboarding, and compliance management.

However, Deel is better suited to medium-to-large global nonprofits, while OnPay is aimed at small-to-medium US-based ones. For instance, Deel includes payroll in 100+ countries where you don’t have an entity, background checks, and immigration support. You might prefer OnPay, however, for its straightforward, affordable pricing plan.

Read the full OnPay review.

OnPay Pricing Plans

  • $40/month + $6/user/month: Multi-state payroll, tax filing, and payments, employee self-service, e-signing, onboarding, PTO management

Compared with other providers like Gusto or QuickBooks, OnPay has only one all-inclusive plan. This is both affordable and simple to plan around. However, you can’t scale features up or down as your workforce changes.

Pros

  • One simple, affordable pricing plan
  • Includes PTO tracking
  • Includes document storage

Cons

  • You can’t scale up or down with plan features
  • No time tracking
  • Limited third-party integrations

The Best Payroll Software for Nonprofits Compared

Best For Standout Features Free Trial Countries Covered Benefits administration Time off management Time tracking
Deel Global nonprofits • Global payroll
• Immigration support
• Time off & expense management
150+
Patriot Software Affordability • Quick payroll and tax filing
• Employee portal
• Report labor costs by department
✅(30 days) 1 (USA)
Rippling Customizing and automating payroll • Grant tracking payroll reports
• Automated compliance checks
• Workflow automation
145+
ADP Best overall payroll for nonprofits • Streamlined payroll and tax filing
• Recruiting tools
• Comprehensive HR add-on modules
✅(3 or 4 months) 140+
QuickBooks Integrating with QuickBooks Bookkeeping • Full-service payroll
• Benefits administration
• Time tracking
✅(30 days) 1 (USA)
Gusto Generous essentials plan • Full-service auto-payroll
• Time and project tracking
• Hiring and onboarding tools
75+
OnPay Straightforward pricing • Auto tax payments
• PTO tracking
• Payroll task delegation
✅(30 days) 1 (USA)

Conclusion – What Is the Best Payroll Software for Nonprofits?

ADP is our standout pick for the best overall payroll software for nonprofits. It offers not only essentials like auto-payroll, tax filing, benefits management, and compliance monitoring—but also employee debit cards, onboarding, and hiring tools.

While its HR modules are as comprehensive as Rippling’s, ADP involves a lower learning curve. Plus, it enables global payroll like Deel while additionally offering time tracking and a generous free trial.

How We Test Payroll Software

We included the following factors when analyzing the best payroll software for nonprofits.

  • Pricing – Providers must offer excellent value for money so nonprofit customers make the most of donors’ money.
  • Features – We ensure platforms have core payroll features, including unlimited payroll runs, tax filing, payment, and compliance checks, plus competitive tools, including benefits and time off management, time tracking, and customizable reports.
  • Integrations – Great payroll software for nonprofits should include multiple integrations with third-party platforms, including accounting and time-tracking software.
  • Automation – Excellent payroll platforms allow nonprofits to save time with workflow automations such as automated compliance alerts.
  • Ease of use – Platforms must be highly intuitive to navigate, with clear feature categorization and easy-to-find tools, to save nonprofits valuable time.
  • Third-party reviews – We factor in user feedback when picking payroll software by checking third-party reviews on websites, including G2 and Capterra.

How to Choose the Best Payroll Software

Bear these points in mind when choosing your payroll platform.

  • Budget – Determine your overall monthly budget for payroll software (say, $100, $500, or $1,000 a month) and prioritize platforms and pricing plans that meet it. Decide which must-have features and nice-to-have extras to include in your budget.
  • Ease of Use – Test user-friendliness in a demo to ensure your team can use the software effectively. For instance, beginner-friendly software is quick to set up and runs payroll in a few clicks, saving you training costs and minimizing payroll errors.
  • Compatibility – Check whether platforms integrate with software you’re already using—such as accounting, time tracking, and hiring software. Some providers limit specific integrations to higher-tier plans.
  • Key FeaturesPrioritize essential features like auto-payroll, tax filing, expenses and time off management, and benefits administration. You may also need tools supporting compliance, time tracking, and hiring.
  • Scalability – Platforms, including multiple plans and add-ons, can scale with your changing workforce. For example, a growing workforce may require one-click time tracking to streamline timesheet approvals and minimize time theft.
  • Customer Support – Check providers’ support hours by chat, email, and phone. Also, read user reviews mentioning support teams’ quality and speed.

FAQs

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Ioana Andrei
Editor

Ioana is a professional writer with bylines in TechRadar, Top10.com, Newsbreak, and The Startup. A former management consultant, trained actor, and playwright, she approaches complex topics with creativity and analytical insight. She writes extensively for businesses, media platforms, and for the stage.