Quick Overview
- 1#1: Gusto - Streamlined payroll and HR platform designed for small to mid-sized nonprofits with easy compliance, unlimited payroll runs, and integrations for nonprofit accounting.
- 2#2: ADP - Comprehensive payroll solutions with nonprofit-specific features like grant tracking, fund accounting integration, and robust compliance for organizations of all sizes.
- 3#3: Paychex - Flexible payroll and HR services tailored for nonprofits, offering tax compliance, multi-state payroll, and reporting for donors and grants.
- 4#4: QuickBooks Payroll - Integrated payroll with QuickBooks accounting, ideal for nonprofits needing seamless W-2/1099 filing and expense tracking tied to funds.
- 5#5: OnPay - Affordable full-service payroll with expert support, custom reporting, and nonprofit-friendly pricing for accurate tax handling.
- 6#6: Patriot Software - Simple, low-cost payroll software with in-house support, multi-state filing, and easy setup for small nonprofits.
- 7#7: Payroll4Free - Free payroll software for nonprofits with under 25 employees, handling direct deposit, W-2s, and basic compliance.
- 8#8: Rippling - All-in-one HR, payroll, and benefits platform with automation for nonprofit employee management and compliance.
- 9#9: Paycor - Cloud-based HCM with payroll tailored for nonprofits, featuring analytics, grant fund allocation, and mobile access.
- 10#10: Paylocity - Modern payroll and talent management suite supporting nonprofit-specific needs like volunteer tracking and customized reporting.
Tools were ranked based on nonprofit-specific features (such as grant tracking, fund accounting integration, and donor reporting), reliability, ease of use, and overall value, ensuring a balanced mix of functionality and accessibility for diverse organizational requirements.
Comparison Table
Choosing the right nonprofit payroll software is key to efficient staff management and alignment with organizational goals; this comparison table explores top tools like Gusto, ADP, Paychex, QuickBooks Payroll, OnPay, and more, guiding readers in evaluating features, costs, and fit for their specific needs.
| # | Tool | Category | Overall | Features | Ease of Use | Value |
|---|---|---|---|---|---|---|
| 1 | Gusto Streamlined payroll and HR platform designed for small to mid-sized nonprofits with easy compliance, unlimited payroll runs, and integrations for nonprofit accounting. | enterprise | 9.4/10 | 9.5/10 | 9.7/10 | 9.1/10 |
| 2 | ADP Comprehensive payroll solutions with nonprofit-specific features like grant tracking, fund accounting integration, and robust compliance for organizations of all sizes. | enterprise | 9.1/10 | 9.4/10 | 8.2/10 | 8.7/10 |
| 3 | Paychex Flexible payroll and HR services tailored for nonprofits, offering tax compliance, multi-state payroll, and reporting for donors and grants. | enterprise | 8.8/10 | 9.2/10 | 8.5/10 | 8.3/10 |
| 4 | QuickBooks Payroll Integrated payroll with QuickBooks accounting, ideal for nonprofits needing seamless W-2/1099 filing and expense tracking tied to funds. | enterprise | 8.0/10 | 8.2/10 | 8.1/10 | 7.4/10 |
| 5 | OnPay Affordable full-service payroll with expert support, custom reporting, and nonprofit-friendly pricing for accurate tax handling. | specialized | 8.6/10 | 8.4/10 | 9.2/10 | 9.0/10 |
| 6 | Patriot Software Simple, low-cost payroll software with in-house support, multi-state filing, and easy setup for small nonprofits. | specialized | 7.8/10 | 7.4/10 | 8.6/10 | 9.1/10 |
| 7 | Payroll4Free Free payroll software for nonprofits with under 25 employees, handling direct deposit, W-2s, and basic compliance. | specialized | 7.2/10 | 6.5/10 | 8.5/10 | 9.5/10 |
| 8 | Rippling All-in-one HR, payroll, and benefits platform with automation for nonprofit employee management and compliance. | enterprise | 8.4/10 | 9.1/10 | 8.2/10 | 7.6/10 |
| 9 | Paycor Cloud-based HCM with payroll tailored for nonprofits, featuring analytics, grant fund allocation, and mobile access. | enterprise | 8.1/10 | 8.4/10 | 7.9/10 | 7.6/10 |
| 10 | Paylocity Modern payroll and talent management suite supporting nonprofit-specific needs like volunteer tracking and customized reporting. | enterprise | 7.8/10 | 8.2/10 | 7.5/10 | 7.0/10 |
Streamlined payroll and HR platform designed for small to mid-sized nonprofits with easy compliance, unlimited payroll runs, and integrations for nonprofit accounting.
Comprehensive payroll solutions with nonprofit-specific features like grant tracking, fund accounting integration, and robust compliance for organizations of all sizes.
Flexible payroll and HR services tailored for nonprofits, offering tax compliance, multi-state payroll, and reporting for donors and grants.
Integrated payroll with QuickBooks accounting, ideal for nonprofits needing seamless W-2/1099 filing and expense tracking tied to funds.
Affordable full-service payroll with expert support, custom reporting, and nonprofit-friendly pricing for accurate tax handling.
Simple, low-cost payroll software with in-house support, multi-state filing, and easy setup for small nonprofits.
Free payroll software for nonprofits with under 25 employees, handling direct deposit, W-2s, and basic compliance.
All-in-one HR, payroll, and benefits platform with automation for nonprofit employee management and compliance.
Cloud-based HCM with payroll tailored for nonprofits, featuring analytics, grant fund allocation, and mobile access.
Modern payroll and talent management suite supporting nonprofit-specific needs like volunteer tracking and customized reporting.
Gusto
enterpriseStreamlined payroll and HR platform designed for small to mid-sized nonprofits with easy compliance, unlimited payroll runs, and integrations for nonprofit accounting.
Automated nonprofit-specific payroll compliance with seamless reimbursements and stipend tracking treated as non-taxable
Gusto is an all-in-one payroll, HR, and benefits platform tailored for small to mid-sized nonprofits, automating payroll processing, tax compliance, and employee management. It supports nonprofit-specific needs like reimbursements, stipends, board member payments, and integrations with accounting tools such as QuickBooks and Aplos. With features for time tracking, benefits administration, and ACA compliance, Gusto simplifies operations while ensuring regulatory adherence for 501(c)(3) organizations.
Pros
- Intuitive interface with quick setup and automated payroll runs
- Robust nonprofit compliance including tax filings, reimbursements, and 1099 handling
- Excellent integrations with nonprofit accounting software and strong customer support
Cons
- Pricing scales up quickly for larger teams or with add-ons
- Advanced grant tracking and fund accounting require third-party integrations
- Limited built-in reporting for complex nonprofit financials
Best For
Small to mid-sized nonprofits seeking a user-friendly, full-service payroll and HR solution without needing extensive IT resources.
Pricing
Simple: $40 base + $6/person/month; Plus: $80 base + $12/person/month; Premium: Custom quote; nonprofit discounts available.
ADP
enterpriseComprehensive payroll solutions with nonprofit-specific features like grant tracking, fund accounting integration, and robust compliance for organizations of all sizes.
Grant and fund allocation tracking that automatically codes payroll expenses to specific funding sources for accurate nonprofit financial reporting.
ADP offers comprehensive payroll and HR solutions tailored for nonprofits through its ADP Workforce Now platform, handling payroll processing, tax compliance, benefits administration, and time tracking. It includes nonprofit-specific features like grant and fund allocation for payroll expenses, multi-entity support for organizations with multiple programs, and automated reporting for Form 990 and donor restrictions. This scalable solution integrates with popular nonprofit accounting software such as QuickBooks, Sage Intacct, and Blackbaud, ensuring seamless financial management.
Pros
- Robust nonprofit-specific tools like grant/fund payroll allocation and compliance reporting
- Scalable for small to enterprise-level nonprofits with strong integrations
- Dedicated support and 24/7 U.S.-based customer service
Cons
- Higher pricing may strain smaller nonprofits' budgets
- Steeper learning curve and longer implementation times
- Custom quotes make upfront cost comparison challenging
Best For
Mid-sized to large nonprofits (50+ employees) needing an enterprise-grade payroll system with HR and compliance features.
Pricing
Custom quote-based pricing; typically $4-$12 per employee per pay period for payroll, plus $50-$200/month base fees and add-ons for HR/benefits.
Paychex
enterpriseFlexible payroll and HR services tailored for nonprofits, offering tax compliance, multi-state payroll, and reporting for donors and grants.
Nonprofit-specific grant reimbursement and multi-fund payroll allocation
Paychex provides comprehensive payroll and HR software tailored for nonprofits, handling payroll processing, tax compliance, direct deposits, and W-2/1099 filings with nonprofit-specific considerations like grant reimbursements and stipends. The platform includes time tracking, benefits administration, and HR tools to manage employees and volunteers efficiently. It ensures compliance with nonprofit regulations, including Form 941 adjustments for exempt organizations, and integrates with popular accounting software.
Pros
- Strong compliance tools for nonprofit tax filings and grant tracking
- Integrated HR and benefits management
- Reliable customer support with dedicated nonprofit specialists
Cons
- Pricing can be steep for very small nonprofits
- Steeper learning curve for advanced customization
- Limited free tier or trial options
Best For
Mid-sized nonprofits needing robust, compliant payroll integrated with HR and accounting systems.
Pricing
Custom quotes starting at ~$59/month base + $5/employee; nonprofit discounts available upon request.
QuickBooks Payroll
enterpriseIntegrated payroll with QuickBooks accounting, ideal for nonprofits needing seamless W-2/1099 filing and expense tracking tied to funds.
Deep integration with QuickBooks Online Nonprofit edition for effortless syncing of payroll data to accounting books
QuickBooks Payroll is an integrated payroll solution from Intuit that works seamlessly with QuickBooks accounting software, automating payroll processing, tax calculations, filings, and direct deposits for businesses including nonprofits. It supports employee self-service portals, time tracking, and benefits management, making it suitable for handling W-2s, 1099s, and compliance needs. While not exclusively designed for nonprofits, it offers reliable general payroll features with some accommodations for nonprofit tax forms and reporting.
Pros
- Seamless integration with QuickBooks accounting for unified financial management
- Automated federal and state tax filings with nonprofit-compatible forms
- Employee self-service portal and mobile app for easy access
Cons
- Pricing can be expensive for very small nonprofits with few employees
- Lacks deep nonprofit-specific features like fund accounting or grant payroll tracking
- Best suited for users already in the QuickBooks ecosystem, limiting flexibility
Best For
Mid-sized nonprofits already using QuickBooks accounting that need reliable, integrated payroll without specialized nonprofit tools.
Pricing
Core: $45/mo + $6/employee; Premium: $80/mo + $9/employee; Elite: $125/mo + $11/employee (nonprofit discounts may apply; billed annually).
OnPay
specializedAffordable full-service payroll with expert support, custom reporting, and nonprofit-friendly pricing for accurate tax handling.
Unlimited payroll runs and expert tax filing handled by OnPay specialists
OnPay is a user-friendly payroll platform tailored for small to mid-sized nonprofits, offering automated payroll processing, tax calculations, and filings compliant with nonprofit regulations like Form 941 and state unemployment exemptions. It includes HR tools, benefits administration, and seamless integrations with accounting software such as QuickBooks and Xero. With unlimited payroll runs and expert support, it simplifies compliance for organizations with variable employee counts.
Pros
- Affordable flat-rate pricing with unlimited payroll runs
- Excellent customer support including payroll experts
- Strong integrations and nonprofit tax compliance
Cons
- Limited built-in time tracking (requires integrations)
- Fewer advanced HR analytics for larger nonprofits
- Setup may require initial assistance for complex multi-state payroll
Best For
Small to mid-sized nonprofits seeking simple, cost-effective payroll without needing extensive enterprise-level features.
Pricing
$40 base fee + $6 per active employee/month; nonprofit discounts available upon inquiry.
Patriot Software
specializedSimple, low-cost payroll software with in-house support, multi-state filing, and easy setup for small nonprofits.
Tax penalty guarantee covering up to $50,000 for errors in filings if using Full Service Payroll
Patriot Software offers affordable online payroll solutions designed for small to mid-sized nonprofits, including specialized handling for clergy housing allowances, designated gifts, and 501(c)(3) compliance. It provides in-house processing, automated tax filings (941s, 944s, W-2s), direct deposit, and basic HR tools like onboarding and time-off tracking. Ideal for organizations seeking straightforward payroll without complex enterprise features.
Pros
- Highly affordable pricing with transparent per-employee fees
- Excellent U.S.-based customer support with live chat and phone
- Nonprofit-specific features like housing allowance tracking and tax guarantees
Cons
- Limited advanced reporting and analytics compared to enterprise solutions
- Fewer third-party integrations (e.g., no native QuickBooks Online sync)
- Basic HR module lacks robust employee self-service portals
Best For
Small to mid-sized nonprofits with 1-100 employees needing simple, compliant payroll without advanced HR complexities.
Pricing
Basic Payroll: $17 base + $4/employee/month; Full Service Payroll: $37 base + $4/employee/month (includes tax filing); Enhanced options add $10-20/month.
Payroll4Free
specializedFree payroll software for nonprofits with under 25 employees, handling direct deposit, W-2s, and basic compliance.
Lifetime free payroll processing for qualifying small nonprofits and businesses
Payroll4Free is a web-based payroll platform designed for small businesses and nonprofits, offering free processing for organizations with up to 25 employees per company. It automates payroll calculations, federal/state tax withholdings, paycheck printing or direct deposit, and generates W-2s and 1099s. While suitable for basic nonprofit payroll needs, it lacks advanced features like fund accounting integration or grant-specific reporting.
Pros
- Completely free for small teams up to 25 employees
- Straightforward setup and intuitive interface
- Handles essential tax forms and multi-state payroll
Cons
- Strict 25-employee limit per company
- Limited integrations and reporting for nonprofits
- No advanced HR or compliance tools for complex orgs
Best For
Small nonprofits with 25 or fewer employees needing a no-cost, basic payroll solution without advanced accounting needs.
Pricing
Free for single-company use with up to 25 employees; optional paid add-ons for direct deposit ($1/check) or multi-company support.
Rippling
enterpriseAll-in-one HR, payroll, and benefits platform with automation for nonprofit employee management and compliance.
Real-time policy engine that automates compliance and payroll rules across all 50 states without manual updates
Rippling is an all-in-one HR, payroll, and IT platform designed to unify employee management, including payroll processing for nonprofits handling staff, contractors, and grant-funded roles. It automates payroll runs, tax compliance, and filings while integrating with accounting software like QuickBooks for nonprofit financial tracking. The platform supports nonprofit-specific needs such as multi-state payroll, 1099 processing, and customizable withholding for exempt organizations.
Pros
- Comprehensive automation for payroll, HR, and compliance reduces manual work
- Strong integrations with nonprofit accounting tools like QuickBooks and NetSuite
- Real-time syncing across HR, payroll, and IT for efficient workforce management
Cons
- Pricing can be high for small nonprofits with limited budgets
- Overkill for basic payroll needs, with a learning curve for advanced features
- Fewer nonprofit-specific templates compared to dedicated solutions
Best For
Mid-sized nonprofits with complex HR and payroll needs seeking an integrated platform.
Pricing
Starts at $8/user/month for core HR, with payroll add-ons bringing total to $10-20/user/month; custom enterprise pricing for nonprofits.
Paycor
enterpriseCloud-based HCM with payroll tailored for nonprofits, featuring analytics, grant fund allocation, and mobile access.
Fund-level payroll allocation to track expenses across grants and budgets seamlessly
Paycor is a full-service HCM platform with robust payroll capabilities designed to meet the needs of nonprofits, including processing for employees, contractors, and stipends for volunteers. It ensures compliance with nonprofit tax regulations, multi-state payroll, and IRS Form 941/990 support. The software integrates HR functions like onboarding, time tracking, and benefits management, making it suitable for organizations managing complex workforce structures.
Pros
- Comprehensive payroll compliance tailored for nonprofits including W-2/1099 and multi-fund allocation
- Integrated HR tools for recruiting, performance, and onboarding
- Strong mobile app and analytics for workforce insights
Cons
- Pricing can be higher than nonprofit-specific alternatives
- Implementation may take longer for complex setups
- Fewer direct integrations with niche nonprofit accounting software like Aplos
Best For
Mid-sized nonprofits seeking an all-in-one payroll and HR solution with scalable features.
Pricing
Custom quote-based; typically starts at $175/month base + $8-12 per active employee/pay period, with nonprofit discounts available.
Paylocity
enterpriseModern payroll and talent management suite supporting nonprofit-specific needs like volunteer tracking and customized reporting.
Grant and fund source payroll allocation with customizable reporting for compliance and auditing.
Paylocity is a cloud-based human capital management (HCM) platform offering payroll processing, HR tools, benefits administration, and time tracking tailored for nonprofits with features like grant-funded payroll allocation and compliance reporting. It supports complex nonprofit structures with multi-entity management and custom fields for funding sources. The software emphasizes mobile accessibility and employee self-service, integrating with popular accounting systems for seamless financial workflows.
Pros
- Robust payroll automation with nonprofit-specific allocation for grants and funds
- Strong mobile app for employee self-service and time tracking
- Excellent customer support and onboarding assistance
Cons
- Pricing can be steep for small nonprofits
- Less specialized nonprofit features compared to dedicated solutions
- Initial setup and implementation may require significant time
Best For
Mid-sized nonprofits needing an integrated HCM platform with reliable payroll and HR capabilities beyond basic processing.
Pricing
Quote-based pricing, typically starting at $20-$40 per employee per month plus base fees and add-ons.
Conclusion
Gusto leads as the top nonprofit payroll software, boasting streamlined operations, HR integration, and robust compliance—ideal for small to mid-sized organizations. ADP and Paychex follow strongly: ADP excels in comprehensive grant tracking and fund accounting for larger groups, while Paychex offers flexibility for multi-state needs and donor-focused reporting. Each tool addresses unique nonprofit priorities, ensuring efficient payroll management alongside compliance.
Take the next step for your organization: explore Gusto to leverage its tailored features and simplify payroll processes, freeing more time to focus on your mission.
Tools Reviewed
All tools were independently evaluated for this comparison