Nonprofit organizations have unique challenges when it comes to managing human resources. From limited budgets to diverse teams and the need to stay compliant with both labor laws and donor expectations, nonprofits often require HR software that is affordable, scalable, and tailored to their specific needs. In this guide, we will explore the best HR software for nonprofits in 2025, helping you find the right tools to improve efficiency, enhance employee engagement, and reduce administrative burdens.
Why Nonprofits Need Specialized HR Software
Nonprofit organizations tend to have a smaller budget and staff compared to for-profit companies. However, that doesn’t mean they should compromise on HR efficiency. Nonprofits still need to manage employee records, track time and attendance, administer payroll, comply with tax regulations, and maintain a healthy workplace culture. The right HR software can streamline these tasks, allowing nonprofits to focus on their mission rather than administrative hurdles.
Additionally, nonprofit HR software should be affordable, easy to use, and flexible to meet the unique demands of the nonprofit sector. The best HR tools for nonprofits can help with:
- Recruitment and onboarding: Attracting and retaining top talent for nonprofit roles.
- Payroll and benefits management: Ensuring employees are paid accurately and on time, while managing benefits.
- Compliance: Staying on top of regulations specific to nonprofits.
- Performance management: Supporting employee development and motivation within a mission-driven environment.
Top HR Software for Nonprofits in 2025
Here are some of the best HR software options specifically suited for nonprofit organizations:
1. Gusto
Best for: Small to mid-sized nonprofits
Key Features:
- Payroll processing and tax filing
- Employee benefits management
- Time tracking and PTO management
- Simple employee onboarding
Why it’s great for nonprofits:
Gusto is an affordable and easy-to-use HR platform that suits nonprofits with smaller teams. It streamlines payroll processing, tax filing, and benefits administration, ensuring that even nonprofit organizations without a dedicated HR team can manage these tasks effectively. Gusto also offers strong customer support and has an intuitive interface, which makes it accessible for users with limited HR expertise. Nonprofits can focus more on their missions while Gusto takes care of administrative tasks.
2. BambooHR
Best for: Growing nonprofits with more complex HR needs
Key Features:
- Employee self-service portal
- Time off tracking
- Performance management tools
- Customizable reports and analytics
- Recruitment and applicant tracking system (ATS)
Why it’s great for nonprofits:
BambooHR is a widely popular HR software solution for small and medium-sized nonprofits. It offers a comprehensive suite of features, including an applicant tracking system (ATS) for efficient recruitment, employee performance tracking, and easy-to-use reporting tools. BambooHR’s customizable interface makes it a great option for nonprofits with diverse teams and complex needs. Its ability to scale as organizations grow is another benefit, allowing nonprofits to expand without outgrowing the software.
3. Zoho People
Best for: Nonprofits seeking an affordable, scalable solution
Key Features:
- Employee database management
- Leave management and attendance tracking
- Performance appraisal system
- Employee self-service portal
- Customizable workflows and reporting
Why it’s great for nonprofits:
Zoho People offers a cost-effective HR solution with many features that can benefit nonprofits. It helps streamline HR processes, such as attendance tracking, leave management, and performance appraisals. Zoho People is also scalable, making it ideal for growing nonprofit teams. The software allows for complete customization, so nonprofits can tailor the platform to fit their specific needs. Additionally, it integrates well with other Zoho products, which can be helpful for organizations already using the Zoho suite of tools.
4. Paycor HCM
Best for: Mid-sized to large nonprofits needing more robust features
Key Features:
- Workforce management tools
- Payroll and tax compliance
- Recruiting and talent management
- Learning management system (LMS)
- Analytics and reporting
Why it’s great for nonprofits:
Paycor HCM is a comprehensive human capital management (HCM) solution that’s especially beneficial for mid-sized and larger nonprofits. Its recruiting and talent management features make it easier to attract top talent for nonprofit roles. Paycor also offers advanced workforce management tools, helping organizations manage employee schedules, track time, and optimize labor costs. Additionally, its learning management system (LMS) allows nonprofits to support employee development and continuous learning, which is essential in fostering a motivated, mission-driven team.
5. Justworks
Best for: Nonprofits looking for all-in-one HR and payroll services
Key Features:
- Payroll and tax filing
- Compliance management (including 501(c)(3) requirements)
- Employee benefits and perks
- Health insurance and 401(k) options
- Employee onboarding and offboarding
Why it’s great for nonprofits:
Justworks offers a streamlined, user-friendly platform designed to handle HR, payroll, and compliance for small businesses and nonprofits. It is particularly beneficial for nonprofits that need to manage compliance with 501(c)(3) regulations and other tax laws. Justworks handles payroll processing, tax filings, employee benefits administration, and provides access to health insurance and 401(k) options. For nonprofits that don’t have the resources to manage these functions in-house, Justworks is a great solution for simplifying HR tasks.
6. ADP Workforce Now
Best for: Large nonprofits with complex payroll and compliance needs
Key Features:
- Payroll and tax administration
- Time and attendance tracking
- Talent management and recruiting tools
- Benefits administration
- Comprehensive reporting and analytics
Why it’s great for nonprofits:
ADP Workforce Now is ideal for larger nonprofits or those with complex payroll and compliance requirements. It offers a robust set of features that include payroll, time and attendance, benefits management, and performance tracking. ADP’s comprehensive reporting and analytics capabilities make it easier for nonprofit leaders to make data-driven decisions. Additionally, ADP has excellent customer support, which can be helpful for nonprofits that need guidance on managing their HR tasks.
Factors to Consider When Choosing HR Software for Nonprofits
Selecting the right HR software for your nonprofit organization depends on various factors. Here are key considerations to keep in mind:
1. Budget Constraints
Nonprofits typically operate with tight budgets, so cost is a critical factor when choosing HR software. Look for solutions that offer flexible pricing or nonprofit discounts. Some providers, such as Gusto or Zoho People, offer affordable plans suited for smaller organizations.
2. Scalability
Your nonprofit will likely grow over time, so it’s important to select HR software that can scale with your organization’s needs. Look for platforms that offer flexibility in adding new features or users as your team expands.
3. Ease of Use
Nonprofits often don’t have dedicated HR staff, so it’s crucial to choose software that is easy to use and doesn’t require extensive training. User-friendly interfaces and customer support can help make the implementation process smoother.
4. Compliance with Regulations
HR software should help you stay compliant with various regulations, including tax filings, 501(c)(3) status requirements, and labor laws. Ensure the software you choose provides the necessary tools to maintain compliance, especially if your nonprofit operates in multiple states or regions.
5. Employee Engagement and Retention
Since nonprofits often rely on passionate, mission-driven employees, fostering a positive workplace culture is essential. Look for software with features that support employee engagement, such as performance management, feedback tools, and training capabilities.
Final Thoughts
Choosing the right HR software for your nonprofit organization is a critical decision that can streamline operations and help you focus on your mission. Whether you need a simple payroll solution or a comprehensive human resources management system, there are plenty of options available to fit your budget and needs. Tools like Gusto, BambooHR, and Zoho People offer affordable, user-friendly solutions for small to medium-sized nonprofits, while larger organizations may benefit from robust platforms like Paycor HCM or ADP Workforce Now.
By investing in the right HR software, your nonprofit can improve HR efficiency, stay compliant, and better support your employees, all while freeing up resources to put towards achieving your organization’s goals.