Best HR Software for Nonprofits & NGOs in 2026
Nonprofits need HR tools that handle grant-funded positions, volunteer management, and tight budgets. We reviewed 10+ platforms to find the 5 best for mission-driven organisations.
Watch: Best HR Software for Nonprofits
What Nonprofits Need in HR Software
Budget-Friendly Pricing
Every dollar spent on software is a dollar not spent on mission. Nonprofits need affordable per-employee pricing, nonprofit discounts, and no hidden fees.
Grant-Funded Position Management
Staff funded by different grants need separate tracking for time, costs, and reporting. Standard HR tools don't handle grant allocation well.
Volunteer & Part-Time Management
Many nonprofits manage a mix of full-time staff, part-time workers, and volunteers. The platform needs to handle different employment types flexibly.
Compliance on a Budget
Nonprofits face the same employment laws as for-profits but with fewer resources. Automated compliance tools are essential to avoid costly mistakes.
Top 5 HR Platforms for Nonprofits
BambooHR
Best Overall HR Platform for Nonprofits
Why It's Best for Nonprofits
BambooHR offers nonprofit pricing discounts, an intuitive interface that non-technical staff can use, and all core HR features without enterprise complexity. Perfect for nonprofits that want modern HR without a big budget.
Key Features
- Employee database & records
- PTO & leave management
- Onboarding workflows
- Performance reviews
Nonprofit-Specific Benefits
- Employee satisfaction surveys
- Applicant tracking
- Document management
- Custom reporting
✓ Pros
- Nonprofit discount available
- Most user-friendly interface
- All core HR in one platform
- Great onboarding tools
- Responsive customer support
✗ Cons
- No built-in payroll (integration needed)
- Limited grant tracking
- No volunteer management module
- Gets expensive at scale
Nonprofits (25-500 employees) wanting affordable, intuitive all-in-one HR
Gusto
Best for Nonprofit Payroll & Benefits
Why It's Best for Nonprofits
Gusto handles complex nonprofit payroll scenarios including grant-funded positions, tax-exempt status, and multi-state compliance. Their benefits marketplace offers affordable options for small nonprofits.
Key Features
- Tax-exempt payroll processing
- Multi-state payroll
- Benefits administration
- Workers' comp
Nonprofit-Specific Benefits
- Time tracking
- Hiring & onboarding
- Tax filing & compliance
- Employee self-service
✓ Pros
- Excellent nonprofit payroll handling
- Affordable benefits marketplace
- Easy to set up and use
- Strong tax compliance
- Good integrations with accounting tools
✗ Cons
- HRIS features are basic
- No grant-time allocation
- Limited to US only
- Performance management is minimal
US nonprofits (5-200 employees) needing affordable payroll and benefits
Rippling
Best for Growing Nonprofits Needing Automation
Why It's Best for Nonprofits
Rippling's automation engine saves HR teams hours weekly on repetitive tasks. For nonprofits with lean HR teams (or no dedicated HR), automated workflows handle onboarding, compliance, and benefits enrollment.
Key Features
- Automated onboarding workflows
- Benefits admin & enrollment
- Time & attendance
- Compliance monitoring
Nonprofit-Specific Benefits
- App provisioning
- Device management
- Custom reporting
- Multi-entity support
✓ Pros
- Best automation saves staff time
- Unified platform reduces tool sprawl
- Scales as organisation grows
- Strong compliance tools
- Modern user interface
✗ Cons
- Higher starting price point
- No nonprofit-specific features
- Modular pricing adds up
- Learning curve for setup
Growing nonprofits (50-500 employees) wanting to automate HR with lean teams
Paychex Flex
Best for Small Nonprofits & PEO Option
Why It's Best for Nonprofits
Paychex offers the most affordable entry point for small nonprofits, with a PEO option that lets tiny orgs access enterprise-level benefits and HR support without hiring an HR team.
Key Features
- Payroll with tax-exempt handling
- PEO option for full HR outsourcing
- Benefits access for small orgs
- Workers' compensation
Nonprofit-Specific Benefits
- Employee handbook builder
- HR advisory services
- Time tracking
- Background checks
✓ Pros
- Most affordable for small orgs
- PEO option for full HR outsourcing
- Good customer support
- Includes HR advisory
- Easy to use
✗ Cons
- Limited HRIS features
- Basic reporting
- Platform feels dated
- Less scalable
Small nonprofits (5-75 employees) wanting affordable payroll with optional HR outsourcing
Paylocity
Best for Mid-Size Nonprofits with Complex Needs
Why It's Best for Nonprofits
Paylocity's community and social features help build culture in mission-driven organisations, while its robust payroll handles multi-grant funding splits and complex nonprofit compliance.
Key Features
- Payroll with grant coding
- Community & social feed
- Benefits administration
- Talent management
Nonprofit-Specific Benefits
- Time & labor tracking
- Learning management
- Expense management
- Custom reporting
✓ Pros
- Community features build culture
- Handles grant-funded payroll splits
- Good learning management
- Strong employee engagement tools
- Comprehensive platform
✗ Cons
- Custom pricing (less transparent)
- Implementation takes longer
- Can be complex for small orgs
- Some features require add-ons
Mid-size nonprofits (100-1,000 employees) with complex payroll and culture-building needs
Quick Comparison
| Platform | Pricing | Payroll | HRIS | Nonprofit Discount | Best For |
|---|---|---|---|---|---|
| BambooHR | $5.25/user | Integration | Excellent | Yes | 25-500 |
| Gusto | $40+$6/ee | Excellent | Basic | No | 5-200 |
| Rippling | $8/user | Built-in | Good | No | 50-500 |
| Paychex | $39+$5/ee | Good | Basic | Contact | 5-75 |
| Paylocity | ~$5/user | Excellent | Good | Contact | 100-1,000 |
Ready to Choose?
Download our Nonprofit HR Software Buyer's Guide with feature comparison matrix, budget planning worksheet, and vendor questions tailored for mission-driven organisations.
View HR Software Comparison