Best Nonprofit Payroll Software
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Compare the Top Nonprofit Payroll Software as of November 2025
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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
BambooHR
BambooHR®
BambooHR Payroll takes the stress out of payday. By combining a single source of data with comprehensive reporting, full-service tax filing, and responsive support, BambooHR ensures employees are paid accurately and on time. With payroll handled, HR can spend less time worrying about compliance and more time focusing on people.Starting Price: $250 per month -
2
RemotePeople
RemotePeople
RemotePeople is a leading Employer of Record (EOR) platform, trusted by top global companies to manage their international workforce. We help businesses efficiently recruit, hire, pay, and manage employees and contractors across 150+ countries, ensuring compliance with local labor laws and payroll regulations. Our platform simplifies global expansion, offering secure and compliant solutions that allow you to confidently scale your team worldwide. Remote People Services: Employer of Record (EOR) Compliantly hire employees in 150+ countries, handling all legal and HR responsibilities. Global Payroll & Benefits Accurate, multi-currency payroll and locally compliant benefits. Contractor Management Onboard, manage, and pay contractors in compliance with worker classification laws. International Recruitment Access top global talent with our expertise. Background Checks Conduct thorough background screenings for secure hiring.Starting Price: $199 -
3
OrangeHRM Free HR Software
OrangeHRM
OrangeHRM provides a world-class HRIS experience and offers everything you and your team need to be that HR hero you know that you are. Whether you are trying to track PTO or hold performance reviews, you get all of the tools you need to shine. Thousands of businesses around the world are benefitting from OrangeHRM as their HR management software. It doesn’t matter whether you are in the start-up stage or a multinational organization, our free & open source HR software, the OrangeHRM Starter version will help you be the HR hero you know you are with powerful HR management capabilities which include: - Employee Management - PTO/Leave Management - Reports & Analytics - Performance Management - HR Administration - Recruitment (ATS) - Time Tracking - Mobile App You can use the OrangeHRM Starter edition on the cloud or download it and host it yourself.Starting Price: $0 -
4
Pebl
Pebl
Velocity Global simplifies global workforce expansion by providing businesses with an easy-to-use HR platform for payroll, compliance, and HR support. With services spanning 185+ countries, we ensure your team can manage international employees efficiently and compliantly. Our platform enables accurate, on-time payroll for global teams while eliminating common errors through a streamlined process. All-inclusive rates incorporate locally mandated taxes and contributions, ensuring compliance and simplifying financial planning. Statutory benefits like pensions and social security are managed by our experts, who enroll employees in the appropriate programs based on their location. -
5
Folks
Folks
Simplify payroll management with Folks Payroll, built for Canadian businesses. Automate calculations, deductions, and government remittances to stay compliant while reducing errors. Employee data, worked hours, and absences flow seamlessly into payroll, ensuring accuracy and efficiency every cycle. With direct deposit, electronic pay stubs, and secure record-keeping, employees get paid on time and with confidence. Folks HR makes payroll stress-free and efficient, so you can focus on what matters most—your people.Starting Price: $6 per employee per month -
6
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 -
7
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 -
8
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 -
9
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 -
10
NolaPro
Noguska
NolaPro is a robust, Linux-based ERP for Accounting, Order Tracking, Inventory Management & Payroll, designed to rival much more expensive choices. It is fully customizable and scalable for any size business, unlike any accounting program available today. The Cloud version allows a "hands-off" approach, but can be downloaded on Linux or Windows platforms for those who prefer to have local control and security. Features include: Credit Card Processing, Fulfillment & Service Order, AP, AR, Inventory, CRM, General Ledger, Payroll, Timeclock, Client Payment Portal and integration with many 3rd party apps -- or request your own! NolaPro is multi-lingual, supports multi-currency, offers tons of options & add-ons, and comes fully loaded with over 150 standard reports. A+ reviews from TechRepublic, The Linux Journal, Entrepreneur Magazine and CNet agree that NolaPro provides flexibility, features and pricing which provide you unparalleled value in managing your business.Starting Price: $0 -
11
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 -
12
Perfect Payroll Management System
SARU TECH
The Perfect Payroll Management System simplifies payroll operations by automating salary calculations, tax deductions, and bonuses to ensure quick, accurate, and secure payroll processing. This enhances employee satisfaction by making payroll operations reliable and straightforward. Key features include simplified employee onboarding, which allows for efficient digital capture of employee details and document management, thus reducing paperwork and errors. The system also provides robust tools for customizing salary components to align with organizational policies, ensuring fair and accurate compensation. Additionally, it facilitates single-click payroll runs to automate various payroll activities, enhancing the accuracy of computations and compliance with tax laws. This system streamlines payroll management, making it easier for businesses to manage employee compensation effectively and efficiently.Starting Price: $5/month -
13
Greenshades
Greenshades Software
Greenshades is the cloud-based, compliance-driven payroll and HR solution that thousands of companies trust. The Greenshades HR and payroll platform is ERP-independent and flexible, allowing for easy set up and long-term in-house functionality. Of course, the Greenshades platform also integrates smoothly with the General Ledger system of Dynamics GP, Dynamics365 BC (Business Central) and F&O (Finance and Operations), as well as older platforms like NAV, SL, or AX. All this ensures you get a truly tailored fit without the expense and overhead of outsourced payroll providers. With robust employee self-service, proactive compliance and comprehensive tax reporting, Greenshades makes HR and payroll easier than ever. We are a payroll provider that has NO float, meaning we do not require pre-funding of payroll tax accounts. And don’t forget: the Greenshades payroll platform also includes our top-rated, end-to-end support, which means our experts are there to help every step of the way. -
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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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15
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 -
16
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. -
17
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 -
18
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 -
19
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) -
20
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. -
21
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. -
22
Netchex
Netchex
Netchex is a cloud-based HCM (Human Capital Management) system designed to help businesses manage the employee lifecycle, from recruitment to retirement, with a range of tools to manage recruiting, hiring & onboarding, plus payroll and tax compliance, human resources, time and attendance, benefits, and more. As a cloud-based solution, Netchex gives users the flexibility to manage the employee lifecycle anytime, anywhere, via any internet-enabled device. Netchex helps users streamline the entire hiring process through their applicant tracking and onboarding system. With Netchex recruiting technology, users can find and evaluate qualified candidates, as well as carry out background checks, send offer letters, archive resumes, and more. Features such as flexible payment options, pre-processing reports and analysis, and compliance management help users manage payroll and tax processes accurately and efficiently. -
23
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 -
24
Sage Intacct
Sage Intacct
Sage Intacct is a premier cloud-based financial management software designed for growing businesses. It offers comprehensive features including core financials, accounts payable and receivable, cash management, and multi-entity consolidations. Sage Intacct's advanced modules cater to complex financial needs, ensuring scalability as your business grows. The software integrates seamlessly with other business applications, providing real-time financial and operational insights. Its user-friendly interface and customizable dashboards empower your team to adapt quickly and make data-driven decisions. Sage Intacct's robust reporting capabilities and automation of key financial processes help improve accuracy, efficiency, and compliance. Trusted by thousands of organizations, Sage Intacct streamlines financial operations, enhances visibility, and drives business growth. With award-winning customer support and continuous innovation, Sage Intacct is your partner. -
25
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 -
26
Square Payroll
Block
Square offers a PC and mobile-friendly app that assists businesses with payroll management. The platform can be used for employees, contractors, or both at the same time, and monthly pricing adapts to the number of people on the payroll. Other additional features include tracking of work hours, automated filing of state and federal taxes, monitoring sick leave, and workers' compensation.Starting Price: $6/month -
27
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 -
28
UZIO
UZIO
Technologies change, but our dedication to enabling businesses in the United States and perfecting their employee experience never will. UPLIFT YOUR HR & WORKFORCE MANAGEMENT WITH UZIO Are your HR administration, payroll processing, and benefits management processes being managed in silos? UZIO a cloud-based SaaS platform provides you with an all-in-one HR, payroll benefits management, and Time & Attendance solution. It is built for businesses of all sizes. Our platform empowers businesses to minimize the hassle of managing HR, payroll, and benefits in silos. This self-servStarting Price: $4.50 per user per month -
29
Zenefits
TriNet
Zenefits is a SaaS cloud-based human resources platform that helps more than 11,000 small and mid-sized companies empower their workforce, manage change and stay compliant. Zenefits' People Platform delivers the most comprehensive, intuitive HR experience in the market. Its HR, Benefits, Payroll and Performance apps combine with advisory services and tightly integrated partner apps to radically simplify HR administration – reducing paperwork and complexity so companies can focus on starting, running and growing their businesses. When new employees are hired, HR professionals using Zenefits only need to complete a few online fields to begin the onboarding process. Employees sign all agreements online, and Zenefits can automatically process their information. When employees leave, HR can remove them from payroll and benefits and initiate COBRA setup with a single process. Zenefits also offers an employee self-service portal.Starting Price: $8.00/month/employee -
30
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.