Best Nonprofit Payroll Software
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Compare the Top Nonprofit Payroll Software as of March 2026
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What is Nonprofit Payroll Software?
Payroll software helps businesses automate the payment of salaries and wages to their employees. It is used to calculate and process payroll payments, manage employee information, and generate reports. It is a convenient and efficient way to ensure that employees are paid on time and accurately. Payroll software typically includes features for generating paychecks, direct deposit, tax filings, generating year-end tax forms (such as W-2s), and maintaining accurate payroll records. Additionally, many payroll software solutions integrate with time-tracking systems, HR management tools, and accounting software to simplify overall business operations and ensure accuracy in payroll processing. Compare and read user reviews of the best Nonprofit Payroll software currently available using the table below. This list is updated regularly.
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1
Rippling
Rippling
Simplify payroll with Rippling—an all-in-one system to manage and pay employees and contractors, no matter where they are located. Rippling lets you run payroll in less than 90 seconds, ensuring timely and accurate pay runs every time. When an employee’s role, compensation, or benefits change, payroll is automatically updated, eliminating manual work and human error. Rippling also automatically calculates your payroll taxes and files them with the right federal, state, and local agencies at the right time, every time. Fully customizable and flexible, Rippling Payroll can support your business’s unique needs and scales with your business.Starting Price: $8 PEPM -
2
RemotePeople
RemotePeople
The full-lifecycle global employment platform built to recruit, employ, and incorporate. Headquartered in New York, we operate across 150+ countries with owned infrastructure and dedicated human support. Our services: EOR and Contractor of Record for compliant international employment. In-house recruiters who source exceptional talent. US PEO for domestic teams. Global Mobility for visas and relocation. Incorporation guidance when you're ready to scale. All with localized benefits, equity support, and payroll across 150+ currencies. Trusted by 3,000+ companies. Every client gets a dedicated account manager. EOR from $199/month. Ranked #1 on G2 for Ease of Use and Best Support.Starting Price: $199 -
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OrangeHRM Advanced
OrangeHRM
Unlock your team's full potential with OrangeHRM, a premier HRMS experience built for the "HR Hero." Our HR software gives you the tools to automate complex processes and master the entire employee lifecycle with confidence. Trusted by thousands of organizations globally, OrangeHRM is the partner you need to make your HR department shine. Whether you are scaling a fast-growing startup or leading a multinational enterprise, our software adapts to your needs with powerful, comprehensive features: -HR Administration -Employee Management -Reporting & Analytics -Mobile App -Recruitment -Onboarding -Request Desk -Leave Management -Time and Attendance -Roster -Performance Management -Career Development -Training -Surveys -Employee Voice -Discipline Offering both cloud-based and on-premise hosting, we ensure that automating your HR operations is always simple, secure, and incredibly efficient. Ready to see these features in action? Try out our free trial today!Starting Price: $0 -
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FreshBooks
FreshBooks
Make invoicing and billing painless for your small business with FreshBooks. A top-rated invoice and accounting software for self-employed professionals and small businesses, FreshBooks offers a fast, easy, and secure way of crunching numbers so companies can focus on doing the work they love. It offers a wealth of powerful features that includes invoicing, expense tracking, time tracking, project management, payment processing, and reporting. FreshBooks also lets users work from anywhere with the Freshworks mobile app.Starting Price: $6.30/month -
5
Buddy Punch
Buddy Punch
Cloud based time clock solution that pre-populates reports for payroll. Employees can punch in on their desktop or mobile devices. Punching in & out is intuitive for your employees & easy for you to view & export time. Employees can clock in using a browser or our Google, iOS, & Android apps. You can view who's working, their GPS position or even limit where they can punch. We integrate with QuickBooks, ADP, Paychex, & SurePayroll while also offering Excel exports. Advanced features such as PTO Accrual Tracking, Punch Rounding, Job Codes, QR Codes, Automatic Breaks, & SSO are all included in our cloud based time clock.Starting Price: $4.49/user -
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Xero
Xero
Xero's payroll software, with its Gusto integration, makes payroll simple for small businesses. Automatically calculate taxes, file payroll taxes, and pay employees with ease, ensuring compliance with federal, state, and local regulations. Xero integrates directly with your account, syncing payroll data for accurate bookkeeping. With features like next-day direct deposit and automated filings, Xero streamlines payroll, saving you time and reducing administrative tasks.Starting Price: $20/month -
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Hubstaff
Hubstaff
Hubstaff is a time tracking software that helps teams log hours, monitor productivity, and automate payments — whether remote, hybrid, in-office, or field-based. Available on desktop, web, and mobile, Hubstaff enables employees to track time against specific tasks and projects from anywhere. Managers get built-in visibility through app and URL usage data, activity rates, and optional screenshots — all configurable by user role. Designed for global, growing and distributed teams, Hubstaff includes built-in productivity monitoring and workforce analytics to help businesses analyze how time is spent, identify inefficiencies, and improve performance — without micromanagement.Starting Price: $4.99/user/month -
8
TriNet
TriNet
TriNet is a leading provider of HR outsourcing solutions built for small and midsize businesses. Its platform combines payroll, benefits, risk management, compliance, and HR technology in one integrated system. Through its PEO (Professional Employer Organization) and HR Plus (ASO) offerings, TriNet helps companies streamline HR administration, stay compliant, and access enterprise-level benefits. Businesses can run payroll efficiently, manage compliance with complex state and federal regulations, and offer competitive employee benefits with ease. The company’s intuitive HR platform also automates time tracking, leave requests, and onboarding. With TriNet, organizations can focus on growth while ensuring their people and processes are supported by expert HR guidance. -
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Payroll Connected
Canadian Payroll Connected
Payroll Connected is Canada's first and only fully automatic payroll processing software. Just tell it how many hours the employee worked, and your payroll is basically done. Using those hours alone, Payroll Connected calculates not only the usual EI, CPP and Income Tax, but also the Statutory Holiday Pay, Overtime and Vacation Pay completely automatically, by your province's unique labour standards. Because it's online, you can process your payroll at any time, on any device with a web browser. And with all this functionality starting at just $12/month for up to 25 employees and unlimited payrolls, it's functional and affordable.Starting Price: $12/month -
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Payroller
Payroller
With Payroller, you get everything you’d ever need to generate Single Touch Payroll reports in one single app. There’s no need for accounting knowledge, costly consultation fees, or complex systems just to stay compliant. Payroller lets you manage staff assignments without a need to pay for a separate rostering app. With built in GPS logging, you can rest assured your team’s at the right gig and ready to rock at no extra cost. Invite your tax accountant to Payroller so they can access your data and reduce your tax-related workload. There’s no need to export and email files and spreadsheets. All businesses with at least 1 employee need to report salary, PAYG and Super information to the ATO. So, they’ve introduced Single Touch Payroll (STP). Set rosters and assign shifts to your employees. Your employees can clock in and out of work and fill out their timesheet on the Employee app. Approve timesheets to add them to your next pay run.Starting Price: $2.99 per user per month -
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All in one, not one size fits all. Do you have too many systems and processes for managing employees? Manual data entry, piles of payroll paperwork and poor integration across systems result in lost productivity and compliance errors. ADP Workforce Now is a cloud-based platform for HR management software, where you can easily manage all of your HR functions — payroll, HR management, workforce management, talent, and benefits — and gain insights across them all. Quickly and accurately process payroll and equip your employees with anytime, anywhere self-service access to their information. ADP Workforce Now® Payroll is the best-in-class, affordable solution that makes payroll and tax filing easy. It’s engineered to help support compliance obligations and is ready to scale as your business grows. See how ADP Workforce Now provides everything you need to get payroll right.
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12
Paycor
Paycor
Paycor modernizes every aspect of people management, from recruiting, onboarding and payroll to career development and retention. For more than 30 years, Paycor has been listening to and partnering with leaders to learn what they need: a comprehensive, unified HR platform, easy integration with third party apps, powerful analytics, and custom technology and support for specific industry needs. That’s why more than 29,000 customers trust Paycor to help them solve problems and achieve their goals.Starting Price: $99 -
13
isolved
isolved HCM
isolved is a provider of human capital management (HCM) solutions that help organizations recruit, retain and elevate their workforce. More than 195,000 employers and 8 million employees rely on isolved's software and services to streamline human resource (HR) operations and deliver employee experiences that matter. isolved People Cloud™ is a unified yet modular HCM platform with built-in artificial intelligence (AI) and analytics that connects HR, payroll, benefits, and workforce and talent management into a single solution that drives better business outcomes. Through the Sidekick Advantage™, isolved also provides expert guidance, embedded services and an engaged community that empowers People Heroes™ to grow their companies and careers. -
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APS Payroll
APS
At APS, our mission is simple: to make payroll and HR easier. Our comprehensive, user-friendly SaaS platform is designed to streamline human capital management for organizations, enabling efficient payroll processing, automated HR workflows, and an enhanced employee lifecycle—all in one place. With decades of industry expertise, APS is your dependable partner, committed to continuous improvement and innovative solutions that meet the evolving needs of our clients. Our clients and partners benefit from personalized service and dedicated support, helping them achieve their goals effortlessly. Businesses choose APS as their trusted workforce partner because of our unwavering commitment to the customer experience, reflected in our 98% customer satisfaction rate. Experience the APS difference—where professional, approachable, and innovative service meets your HCM needs.Starting Price: $50.00 base fee per month -
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OnTheClock
OnTheClock
OnTheClock is a modern Time Clock Software that helps business owners stay in compliance by tracking employee hours worked. The cloud-based time tracking system automatically calculates and logs employees' punch in and punch out times to display accurate time cards for payroll. Streamline your payroll process by integrating OnTheClock with your payroll software. Quickly export time card data to your payroll provider or easily allow accountant access to your time clock data via email invite. The user-friendly dashboard also allows business owners and admins to manage PTO. Receive, approve, or deny paid time off requests sent by an employee through the time clock system. Additionally, experience a variety of robust employee time clock features such as GPS, scheduling, job and product costing, and much more.Starting Price: $5 base fee + $4 per employee -
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QuickBooks Online
Intuit
QuickBooks Online is the most popular accounting software in the world. QuickBooks Online makes accounting easy. Make tracking receipts, income, bank transactions, and more feel simple with the #1 small business accounting software. Snap photos of your receipts and link them to expenses right from your phone. Our agents are ready and available to answer all your QuickBooks questions. Use the apps you know and love to keep your business running smoothly. QuickBooks Online works on your PC, Mac, tablets, and phones. Click the link above to get a 30 day free trial and 50% off your first 3 months. More than accounting software. QuickBooks helps you track income, expenses, and stay ready for taxes. Customers find on average $3,534 in tax savings per year. Need more help? QuickBooks Live helps you stay organized and be ready for tax time. QuickBooks comes with a mobile app that help you run your business on the go—anytime, anywhere.Starting Price: $9/month (normally $15/month) -
17
BambooHR
BambooHR®
BambooHR® is an award-winning, people-first HR platform with an intuitive design that scales with your business. It centralizes all your HR data in one secure system so you can focus less on paperwork and more on what matters most—your people. With BambooHR, you can: • Hire and onboard top talent seamlessly • Manage all your employee data and records in one place • Run payroll and administer benefits with confidence • Track time, manage performance, and measure employee engagement • Gain actionable insights with AI-powered analytics and reporting • Connect your favorite tools with seamless integrations By consolidating HR processes into one intuitive system, BambooHR empowers you to elevate the employee experience, drive business growth, and simplify HR management.Starting Price: $250 per month -
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Timesheets.com
Timesheets.com
Timesheets.com provides everything you need to track time and expenses in a single, powerful solution. Our easy-to-use service can track billable time, time for payroll, time-off, expenses and HR documents. Perfect for any small to mid-sized business, Timesheets.com can be setup in minutes and comes with free, unlimited live support by phone, email or chat. Try us for free today.Starting Price: $4.50 per user per month. -
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factoHR
factoHR
ffactoHR is a comprehensive, cloud-based HR payroll software in India designed to simplify HR operations and empower organizations to focus on what matters most—nurturing talent and driving success. Trusted by over 3,500 businesses and 2.6 million employees, including industry leaders like Wipro, Siemens, Tata Steel, GHCL, and Cycle Agarbatti, factoHR streamlines HR processes and enhances productivity. Our scalable platform offers a suite of integrated solutions, including HR & Payroll Management, Attendance and Leave Management, Performance Management, and Talent Acquisition, among others. By automating routine tasks, factoHR helps HR teams save time, reduce errors, and focus on strategic initiatives. factoHR’s mobile-first design ensures real-time access to HR data, making it easy for both HR teams and employees to stay informed and manage their information on-the-go. -
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Deel
Deel
Deel is the global HR platform for onboarding, hiring, and paying your international workforce. Manage global hires, contracts, payroll, compliance, and team engagement from one central dashboard. • Hire contractors and employees in over 150 countries • Generate and sign e-contracts tailored to local labor laws and reviewed by Deel's network of legal partners • Automatically collect documents, permits, and ID verification • Offer full payment flexibility for your team across 120+ currencies and 10+ payment methods • Track and approve time off and expense requests • Simplify accounting with automatic invoicing and API integrations with top accounting software • Access 24/7 support for your team in 10 different languagesStarting Price: $49 per contractor/month -
21
TimeCamp
TimeCamp
Discover how a feature-rich free time tracker can end your project management headaches. Let your team perform at its best without intrusive micromanagement. Are you struggling to keep track of your team's performance across different projects? Say "goodbye" to spreadsheets and guesswork. Let TimeCamp do the time tracking and focus on the work that matters. Learn how a piece of time tracking software can help you optimize your team's workflow as well as keep your projects within their budgets. Start working smart by employing TimeCamp to become your own project manager. Access all of the essential information about your projects in one place. Easy! Why waste countless hours on additional data processing just to have a precise report? TimeCamp does it all automatically so you can maintain your focus on the important work.Starting Price: $6.30 per user per month -
22
Time Clock Wizard
Time Clock Wizard
Schedule Employees with alternating work days, pay rates & reimbursements. Track employee work hours accurately. Collect absences, late clock-ins & more. Instant customizable mobile & email alerts to employees & managers. Easily track employee time & generate payroll reports quickly. Fully supports the latest versions of iOS & Android operating systems. Now, your staff can clock in from a single device and location, improving efficiency and accountability. Turn any tablet into a wall-mounted or desktop time clock.Starting Price: $14.95/month -
23
UKG Pro
UKG
UKG Pro is our award-winning human capital management (HCM) solution that helps simplify complex HR processes and provide powerful insights about your workforce. Marrying deep functionality and artificial intelligence (AI) technology with an intuitive, best-in-class user interface, UKG Pro makes it easier for HR and business leaders to optimize performance and improve work experiences for their people. From big-picture data to zooming in to the individual employee’s journey in a matter of seconds—UKG Pro can support even the most complex organizational needs in HR, payroll, time, and talent. Gain one, comprehensive view of all your employee data, including insight into your global teams. Discover the most powerful payroll engine in the industry today, and simplify the most complex tax processes. Deliver a personalized, candidate-centric experience to potential employees, and make it easier for recruiters to assess the right fit. -
24
greytHR
Greytip Software Private Limited
The greytHR Platform is a suite of cloud HR solutions for small and medium enterprises (SMEs). It offers productivity tools for better people management, simpler HR processes, and professional delivery of HR services. The Employee Portal for the manager and employee self-service leads to better employee engagement and all-around time savings. The greytHR software is used by 20,000+ customers and 2 million users in India and the Middle East. Salient Features: ● Core HR ● Onboarding software ● Employee lifecycle management ● Leave & Attendance management ● Payroll management (for India and Middle East) ● 100% HR Compliances (for India & Middle East) ● Document management ● HR Reports and Analytics ● Employee Portal and mobile app ● Integrations & REST API. greytHR is much more than just great software. We take pride in our passionate service, a vibrant HR community, and helpful learning resources.Starting Price: $30 for GCC, ₹3495 for India -
25
Paylocity
Paylocity
Stay ahead of industry trends and client needs with a homegrown, single-database software platform. Rely on seamless implementation that leads to a dedicated Account Manager and service team unlike other providers. Use the same solutions Paylocity uses every day to drive engagement, collaboration, and success. Give administrators, supervisors, and employees the functionality to increase efficiency of daily activities. Connect Paylocity with other business systems to effortlessly flow data across the tools you use most. Headquartered just outside Chicago, Paylocity has revolutionized the marketplace for payroll and human resources professionals for more than 20 years. As HR and payroll professionals, you are the touchpoint between businesses and their employees during this public health emergency. Consider us your resource as you navigate the impact and a new way of operating. The coronavirus pandemic is shifting the daily reality for us all. But we're in this together. -
26
Namely
Namely
People are complex, but your HR solution shouldn’t be. Namely gives you the resources to make your life easier and your employees happier. With modern, intuitive technology and a world-class team of HR experts, Namely empowers people teams with a complete HR solution designed for mid-sized businesses. Namely streamlines all of your HR data into a single platform with an interface you AND your workforce will love to use. Your platform is implemented with your unique business needs in mind. Whether you’re transitioning from a PEO or on the hunt for a new HCM software, Namely has the technology and people to support your company every step of the way. -
27
skillaHR
Vizenta AI
skillaHR - AI Powered HRMS: This HR and talent management tool uses advanced AI to efficiently handle tasks like onboarding, attendance, leave management, and payroll. With its AI capabilities, HRMS supports businesses in identifying and hiring the best talent, while also preparing teams for future challenges. Moreover, it offers features that enhance employee skills and engagement, contributing to better productivity and loyalty. -
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Paychex Flex
Paychex
Paychex Flex is an all-in-one HR software solution that you can build on as your business grows or changes. Use it to run payroll and integrate your HR administration, retirement, and insurance management with service the way you want it and our expert knowledge of the regulations that could affect your business. The more HR functions you bring to Paychex Flex, the more accuracy and efficiency you’ll gain. It can help you: • Recruit and track the best candidates • Streamline hiring and onboarding • Deliver key HR information through custom compliance documents, compensation summaries, performance reviews, company training, and more • Manage health insurance, including compliance support • Administer employee benefits • Track time and attendance data • Pay employees and file and pay your taxes • Plan for retirement, from testing, to real-time reports, and participant enrollment and management -
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Personio
Personio GmbH & Co. KG
Personio is the People Operating System for small and medium-sized companies with 10 to 2,000 employees. Based in Munich, Madrid, London, Dublin, Amsterdam, Berlin and Barcelona, Personio’s mission is to make HR processes as transparent and efficient as possible so HR can focus on what matters most: people. Personio does that by offering an all-in-one HR software that includes human resources, recruiting and payroll, enabling HR to go beyond HR. Thanks to People Workflow Automation technology, Personio helps more than 6,000 customers across Europe to remove delays and realize opportunities. Companies such as Spendesk, Futurice, and Premier Inn are already successfully using Personio to improve their people operations and boost the employee experience.Starting Price: €2.88/month per employee -
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Tillpoint
Tillpoint
Tillpoint is the multi-award-winning EPOS system capable of running your entire business. Its innovative modular design allows users to easily manage all areas of operation, including the POS, Inventory, Staff and Accounting. Tillpoint currently has over 25 modules, all of which are included in the subscription plans, resulting in a complete, centralised, and cost-effective all-in-one solution. The cloud-based system was developed with scalability in mind and is suitable for all sized businesses across a range of industries, particularly hospitality, retail and services. Multi-store businesses, such as chains or franchises, will have access to the hierarchy feature, which allows businesses to easily manage and control simple to complex organisational business structures with accompanying access privileges. Support and training are included as part of the subscription, as well as free lifetime software updates and full access to all future features and modules.Starting Price: $29/month
