7 Best HR & Payroll Software for Non-Profits (2026)
We compared 7 top tools for this category. Gusto is our #1 overall recommendation, boasting a 4.7/5 rating and excelling at non-profit pricing. If you are looking for an alternative specifically for mission-driven teams, BambooHR is a highly capable runner-up.
Gusto
Offers special non-profit pricing and simplifies grant-funded position tracking and donation-based payroll.
Runner Ups
BambooHR
Mission-driven teamsExcellent for keeping track of certifications, volunteer databases, and performance reviews in mission-driven teams.
- Certification tracking
- Great reporting
- Employee happiness focus
- Expensive for small NGOs
- Separate payroll
Starting at
Custom pricing
Nonprofit+ (Acumatica)
Fund accountingAn ERP-level tool for non-profits needing deep fund accounting, grant management, and payroll in one.
- Advanced fund tracking
- Integrated ERP
- Compliant
- High complexity
- Long implementation
Starting at
Custom pricing
Patriot Software
Low budget NGOsThe most affordable full-service payroll option for small non-profits with a simple interface.
- Very cheap
- Fast processing
- US-based support
- Few HR features
- Basic reports
Starting at
$17/mo
TriNet
PEO benefitsA PEO that offers non-profits access to corporate-level healthcare and liability protection.
- Superior healthcare
- Risk management
- Full compliance
- High per-employee cost
- Less control
Starting at
Custom pricing
Paylocity
Hourly staffStrong workforce management for non-profits with hourly staff and varied schedules across programs.
- Great mobile app
- Social features
- Reporting
- Complex setup
- Customer support lag
Starting at
Custom pricing
Justworks
HR consultingSimplifies payroll and benefits while providing access to certified HR consultants for regulatory advice.
- Simple pricing
- Certified HR help
- Auto-compliance
- Minimum employee limit
- No internal ATS
Starting at
$59/user
Related Comparisons
Frequently Asked Questions
Common questions about choosing the right software.
Based on our analysis of 7 options, Gusto is the best overall choice for non-profits, earning a 4.7/5 rating. Key strengths include Easy UI and Direct integration. For a different focus, BambooHR (4.6/5) is a strong alternative specializing in mission-driven teams.
Gusto (4.7/5, From $40/mo) is best for non-profit pricing, while BambooHR (4.6/5, Custom pricing) excels at mission-driven teams. Gusto takes the top spot overall, but BambooHR is the better pick if your priority is specifically mission-driven teams.
While none are entirely free, BambooHR starts at Custom pricing, making it the most budget-friendly option. Most hr & payroll software in this roundup offer free trials so non-profits can evaluate before committing.
Key criteria for non-profits include: non-profit pricing, mission-driven teams, fund accounting. Our #1 pick Gusto leads in non-profit pricing, while Nonprofit+ (Acumatica) (4.5/5) is a noteworthy option for fund accounting. Consider your specific workflow needs and budget to narrow down the best fit.
In this comparison of 7 tools, pricing ranges from Custom pricing (BambooHR) at the low end to premium enterprise tiers. All tools require a paid subscription, though most offer free trials. For the best balance of features and value, we recommend Gusto at From $40/mo.