Payroll Software for Nonprofits
Built for Nonprofits, Designed for Impact
Simplify payroll and time tracking so you can stay focused on your mission.
In a nonprofit, HR moves as fast as the needs you serve, and keeping up can feel overwhelming. You’re balancing limited resources, constant staffing changes, grant-driven requirements, and strict compliance obligations. Ensuring accurate records while supporting employees across multiple programs, roles, and locations is time-consuming, and leaves you with little time to focus on the people and mission that matter most.
72%
72% of nonprofits report that funding reporting requirements are complex and time consuming.
63%
63% of organizations struggle with spreadsheets or different software systems to store and manage payroll and HR data.
19%
19% of nonprofit employees turnover within the first year, nearly double the average for all industries.
Focus on your mission, let our nonprofit payroll specialists handle the rest.
Payroll Support You Can Trust
From onboarding to ongoing support, get fast, reliable service from specialists who understand the unique demands of mission-driven organizations.
- Partner with a team that understands the challenges of nonprofit payroll, while benefiting from U.S.-based service.
- Access support your way — through the PrimePay Hub, by phone, or via chat — for quick, flexible help whenever you need it.
- Offload complex wage calculations to us with our managed payroll option.
Time tracking for your mission just got easier.
Scheduling Made Effortless
Empower your nonprofit with time tracking built for transparency and compliance. Capture every hour worked to ensure accurate labor allocation, reporting, and workforce accountability.
- Ensure accurate pay by storing hourly, overtime, exempt/nonexempt rules, and grant-specific labor rates in time & attendance.
- Manage scheduling across departments, programs, and locations.
- Maintain verifiable, audit-ready time tracking with geofencing, ensuring employees and volunteers clock in and out only from approved nonprofit sites or service locations.
Spend more time driving impact, not on payroll.
Payroll That Supports Your Mission
Process payroll with fewer errors, allocate labor costs by fund, and export financial data-saving time, ensuring accuracy and reducing administrative stress.
- Manage payroll for full-time staff, part-time employees, contractors, and grant-funded roles, with built-in error detection.
- Accurately calculate overtime, stipends, differentials, and grant-funded hours for diverse nonprofit positions.
- Export General Ledger and Journal Entries to your finance tool of choice.
What Our Clients Say About Us
All a Nonprofit Needs in One Place
Payroll
Automated, compliant payroll that streamlines tax filing, worker’s comp, and built in error alerts.
Learn About Our Payroll SoftwareTime & Attendance
Payroll-connected tracking that manages time off, holidays, accruals, absences, and scheduling.
See Our Time Functionality in ActionCompliance
Integrated add-on services that automate record-keeping & reporting and makes HR legally compliant.
Applicant Tracking
Intuitive online recruiting that simplifies job postings, and manages applicants & hiring of employees.
Learn More About Applicant TrackingHR & Onboarding
HR Services that you need and expect like Performance Management, Learning Management, and HR Legal Advice.
Learn More About Our HR SoftwareBenefits Services
Comprehensive employee programs, refined for modern workforce needs, delivering confidence and compliance.
See Our Benefits Admin Capabilities
Frequently Asked Questions
How can payroll software help nonprofits manage labor costs?
Payroll software helps nonprofits manage labor costs by automating time capture, stipends, and overtime, while providing visibility into payroll and deductions. Real-time payroll data gives nonprofits clear insight into how labor spending aligns with budgets, programs, and restricted funds—helping avoid overspending and ensuring compliance with funder requirements. By connecting payroll with time tracking, nonprofits can maintain accurate cost allocations across programs and funding sources.
How does payroll software streamline wage calculations and compliance in nonprofits?
Payroll software automates complex wage calculations, including overtime, stipends, multiple pay rates, and grant-specific labor rules. It supports compliance with FLSA, state labor laws, and nonprofit-specific reporting needs by accurately applying pay rules to each employee, program, and funding source. Automated tax filing, real-time error detection, and compliance alerts help nonprofits avoid costly mistakes and reduce administrative burden.
What payroll challenges do nonprofits face most often?
Payroll teams often navigate multiple pay types, restricted fund rules, reporting requirements, and staff working across several programs. These complexities make manual payroll error-prone—making automation essential for accuracy and compliance.
Do nonprofit organizations typically have dedicated payroll teams?
Many nonprofits operate with small or shared HR/payroll teams, and some rely on staff who manage payroll alongside multiple other responsibilities. Because nonprofits must track program-specific labor, funding restrictions, and grant compliance, dedicated payroll oversight—internal or external—is crucial to minimizing errors and protecting funding.
How does payroll software improve efficiency in nonprofit operations?
Payroll software reduces administrative workload by automating calculations for overtime, stipends, grant allocations, and tax updates. By pulling accurate time data directly into payroll, nonprofits eliminate manual entry, reduce rework, and ensure employees are paid correctly. This allows HR and finance teams to focus more on mission-driven work instead of administrative tasks.
How does payroll software help nonprofits attract and retain staff?
Accurate, predictable pay is essential for retaining nonprofit teams, especially when resources are limited. Payroll software supports retention by eliminating errors, ensuring consistent pay, and providing employees with self-service access to pay information. When staff trust their pay is accurate—and program allocations are correct—organizations build credibility and reduce turnover.