10 Best Payroll Software for Nonprofit Organizations [2026]

Complex payroll tasks like maintaining tax compliance, tracking time for various worker classifications, and managing grant-restricted budgets can be time-consuming and laborious, contributing to burnout. And without the right tools to benchmark compensation, nonprofits don’t have visibility into how competitive their rates are.

The best payroll software for nonprofit organizations simplifies these complexities, enabling teams to focus on fulfilling their mission and supporting their people rather than filling out spreadsheets or stressing over compliance.

In this article, we’ll break down the top 10 platforms that let nonprofit staff reclaim their time and level up worker support, with features like automated and fully compliant payroll runs, comprehensive tax services, reporting tools that make budget tracking easier, and more. We also include pricing details so you can select the platform that fits your budget.

Best payroll software for nonprofit organizations in 2026

Here are the best nonprofit payroll software solutions on the market today. The platforms are listed for comparison, not ranked in any particular order.

Best for: All-in-one HR, payroll, and expense management

Paylocity unifies HR, payroll, and expense management into one platform, helping teams simplify workforce management and reduce costly delays. It’s one of the best payroll software for nonprofit organizations, whether you’re a local organization with a few employees in one location or a multi-entity organization managing thousands of workers across state lines.

The platform simplifies payroll for various worker classifications and funding sources across locations, supports holistic compliance with real-time regulatory reporting, eases tax compliance and exemption filing with expert guidance, and more. It features a marketplace of over 400 seamless integrations, including benefits providers, background check apps, and grant allocation management systems.

Beyond payroll administration, Paylocity helps nonprofit teams overcome their biggest hurdles. It streamlines repetitive and complex processes, supports recruitment and retention through a consumer-grade onboarding experience and compensation benchmarking, and helps teams build a mission-centric culture, all with AI-powered insights, workflow automation, and assistance.

Key Features:

• Automated Form 990 compensation reporting: Paylocity automatically creates real-time, tax-ready compensation reports so that you have all the payroll data you need when it comes time to file Form 990.
• General ledger mapping and third-party integrations: Paylocity integrates with financial systems like QuickBooks and Sage Intacct, as well as ERPs like Oracle NetSuite so you can connect payroll data directly to your main accounting software. Users can also set up general ledger mapping with the help of a dedicated support team.
• Multi-classification management: Manage pay, time tracking, scheduling, retention, and more, all in one place for workers of any classification, from W-2 employees and 1099 contractors to volunteers and seasonal workers.
• Grant-linked payroll tracking: Keep your expenses in order and track budget utilization with software that links payroll runs to specific grants.
• Mobile time and attendance: Easily and accurately track, monitor, and approve time and attendance with a consumer-grade mobile app, ensuring timely and accurate payroll runs across all worker classifications.

Pricing: Custom pricing available with a free demo

2. SurePayroll

Best for: Simple compliance for small nonprofits

SurePayroll (by Paychex) is a cloud-based platform that provides payroll services to nonprofits and small businesses. It provides tools for automatic payroll processing for both W-2s and 1099s on top of direct access to nonprofit tax specialists. It also automates payroll tax compliance at all levels while applying FUTA exemptions for qualified organizations.

SurePayroll’s nonprofit-specific service offerings and emphasis on automation make it a solid choice for small nonprofits that need to streamline compliance. Reviewers appreciate how the platform simplifies compliance tasks and payroll processing, but note billing errors and challenges with customer service.G2 - SurePayroll Review

Key Features:

• Automatic 501(c)(3) FUTA tax filing and exemptions: SurePayroll automatically calculates, files, and submits fully-compliant payroll taxes at the local, state, and federal levels. It calculates and applies FUTA exemptions for qualified 501(c)(3) nonprofit organizations.
• Automatic payroll: Automate payroll with SurePayroll’s Auto Payroll feature, which handles everything in the background without the need for any manual input post-setup. It sends notifications 24 hours in advance of approval and can be turned off with one click.
• Direct access to dedicated nonprofit tax specialists: SurePayroll provides access to a US-based network of specialists who can help you navigate common nonprofit tax filing challenges, such as determining qualification for FUTA exemptions, classifying workers correctly, and adjusting to flexible pay schedules.

Pricing: Plans start at $29/month + $7/employeeSurePayroll Pricing

3. Justworks

Best for: Enterprise-grade health benefits

Justworks is a professional employer organization (PEO) that provides payroll, recruitment, and compliance tools. They provide robust tax filing services and employer-of-record services that make payroll for nonprofits simple, alongside helping budget-constrained small organizations access premium, enterprise-grade benefits.

Reviewers praise that platform’s intuitive UI and most note that their customer support team is very helpful, providing assistance whenever needed. However, they point out that the platform has a few noteworthy limitations compared to competitors, like limited reporting features, clunky admin tools, and a lack of customizability for complex and specific workflows.G2 - Justworks Review

Key Features:

• PEO for multi-state remote staff: Justworks acts as an employer of record for your staff, so you can hire remote employees in different localities easily. Nonprofits can expand into other states without registering there for tax filing purposes.
• Automated multi-state tax locality filing: Justworks withholds, reports, and remits your payroll taxes for you across 4,000 different localities with compliance support across multiple states.
• Compliance support for mixed employee and contractor teams: Pay W-2 employees and 1099 contractors in one platform, providing resources for worker classification support and risk management options (such as workers’ compensation coverage and EPLI).

Pricing: Plans start at $8/month/employeeJustworks Pricing

4. Checkwriters

Best for: Personalized customer support

For organizations looking for nonprofit payroll software that adapts to their specific needs, Checkwriters is a solid choice. They provide automatic payroll processing tools, compliance updates and reports, a centralized employee data repository, and a recruiting and onboarding tool that comes with an integrated applicant tracking system.

Checkwriters also comes with a robust employee self-service portal. Nonprofits can also use Checkwriters as an HR tool to handle performance reviews, check-ins, and goal setting through the platform. Reviewers generally praise Checkwriters for how helpful and supportive their expert staff are, but room for improvement in the platform’s reporting functionality.G2 - Checkwriters Review

Key Features:

• Audit-ready financial reporting for boards: Build detailed monthly or quarterly reports for financial data with dozens of standardized templates that simplify preparation and support auditability.
• Automatic nonprofit-specific regulatory updates: Checkwriters provides updates for any changes in nonprofit-specific regulations, helping organizations proactively stay compliant and avoid fines.
• Centralized data for volunteers and paid staff: Checkwriters provides an HRIS that lets nonprofits bring all their employee records into a single system, whether they’re W-2 employees, 1099 contractors, or FLSA volunteers.

Pricing: Custom

5. OnPay

Best for: Budget-conscious organizations

OnPay provides nonprofit payroll services, specialized HR tools (for recruiting and onboarding), and benefits administration support. For 501(c)(3) organizations operating on a tight budget, this platform offers a strong suite of services, including: expert-led tax services, multi-state compliance support, and payroll tools that let you pay volunteers and board members in addition to W-2 employees and 1099 contractors.

OnPay also integrates with some time-tracking and accounting systems, so you can sync data and reduce tedious double-entry bookkeeping. Users appreciate the platform’s ease of use and simplified onboarding, but also note that its integrations are limited, with many wishing for a native time-tracking system.G2 - OnPay Review

Key Features:

• Unlimited payroll runs included in a single monthly base fee: Make the cost of payroll administration predictable with unlimited payroll runs (including off-cycle payments for bonuses, reimbursements, and corrections) for one consistent baseline fee that depends on the number of employees you have.
• Seamless payment for 1099 contractors: Pay contractors in the same place you pay your W-2 employees and cut out administrative work with automated 1099 filings and a self-service platform.
• Payroll tax services: OnPay’s team of experts withholds and files taxes on your behalf at the federal, state, and local levels, and files for exemptions for qualified organizations.

Pricing: Plans start at $49/month + $6/employeeOnPay Pricing

6. Gusto

Best for: Seamless integrations 

Gusto offers robust payroll services for nonprofits, enabling organizations to integrate data from a wide range of third-party apps, including nonprofit-specific tools like Aplos and MonkeyPod, as well as popular accounting tools like QuickBooks and Xero. The platform includes payroll processing tools, automated tax filing capabilities, and benefits administration software, each designed for ease of use and compatibility with small organizations. 

This platform also provides specialized payroll and HR services for specific nonprofit types, including churches and schools. Reviews show appreciation for Gusto’s general efficiency, especially its automated payroll and recruitment systems, but point out limited customizability for complex payroll scenarios.G2 - Gusto Review 

Key Features:  

• Native bi-directional sync with Aplos fund accounting: Gusto integrates with Aplos, allowing nonprofits to automatically sync payroll data as journal entries and map payroll costs directly to specific funds. 
• Integrated employee-led donation and giving tools: Gusto supports nonprofits and 501(c)(3)s (including 820,000+ charities in the US) through Gusto Giving, which lets employees donate to nonprofits of their choice directly from their paycheck. 
• Automatic grant-required new-hire reporting: This platform automatically files legally mandatory new-hire reports (including for contractors) to maintain compliance with federal, state, and grant-specific requirements 

Pricing: Plans start at $49/month + $6/employeeGusto Pricing

7. Paycor

Best for: Easy-to-use payroll and compliance tools 

Paycor is an HCM platform providing payroll and HR solutions for nonprofits. The platform’s payroll features include on-demand pay, automatic payroll runs, tax filing services, and a compliance dashboard that provides proactive alerts. 

Teams can also use Paycor to recruit talent and keep track of their budget with detailed analytics. Paycor is known for its ease of use across the board, but many reviewers point to feature limitations (like limited customizability for reporting and a more rudimentary mobile app) and issues with customer support.G2 - Paycor Review

Key Features:  

• Proactive compliance alerts: Paycor provides compliance warnings to help teams identify and resolve potential issues ahead of filing, from missing data to recommendations at the federal, state, and local levels. Alerts are funneled into a centralized dashboard, making it easy for nonprofits to spot compliance gaps and keep up with changing requirements. 
• Built-in time management tools: Employees and volunteers can track their hours against specific projects, track their total hours worked, and request time off in one spot. Meanwhile, management teams get automated timecard approvals and AI insights to help optimize labor spend and plan budgets. 
• Reporting tools for deep insights into employee data: Paycor’s reporting tool helps nonprofits measure and benchmark employee data, enabling organizations to optimize labor allocation, pay competitive rates, and focus on retention.

Pricing: CustomPaycor Pricing

8. QuickBooks Payroll

Best for: Fund accounting integration

QuickBooks Payroll is a convenient option for nonprofit accountants already using the QuickBooks suite, as it integrates directly with QuickBooks Online. The platform features integrated time tracking, automatic and fully compliant payroll processing, 1099 filing support, and more.  

QuickBooks lets users map their expenses directly to specific grants and funding programs with the “class tracking” feature, create reports to track grant-restricted fund availability, and sync data with nonprofit-specific apps like Fundly. Users appreciate the native integration with QBO, but find that their customer support can be unresponsive.G2 - QuickBooks Payroll Review

Key Features:  

• Native "Class" and "Program" tracking synchronization: QuickBooks’ class tracking feature lets you assign specific classes (such as grants) to your employees and generate per-class payroll summary reports that update in real time. 
• Integrations with fundraising software: QuickBooks integrates with nonprofit fundraising solutions, like Fundly, for example. Integrating Fundly lets nonprofits sync their donation and transaction records into QuickBooks. 
• Grant-restricted fund balance reporting for transparency: Nonprofits can use "classes" when running payroll to link expenses directly to specific grants and create balance reports that show how much of the funding has been utilized at any given time. 

Pricing: Plans start at $88/month + $6.50/employee/monthQuickBooks Payroll Pricing

9. Paychex

Best for: Small nonprofits needing scalable HR 

Paychex is a payroll, HR, and benefits administration platform best fit for small but growing organizations where scalability is a priority. The platform enables simplified payroll compliance, comprehensive, customizable financial reporting, and automated tax filing. These, combined with an employee self-service platform, help reduce the administrative burden on nonprofit leaders and financial teams operating in growing nonprofits. 

Paychex also helps organizations access capital through unpaid invoices with Paychex Funding Solutions, allowing nonprofits to cover operational expenses without dipping into grant-specific funds. User reviews praise the platform for how well it simplifies payroll, but note limitations such as dysfunctional time clocks, customer service issues, and occasional processing errors.G2 - Paychex Review

Key Features:  

• Dedicated nonprofit compliance and HR support: Paychex helps nonprofits simplify compliance by providing a dedicated expert for real-time assistance, notifications for relevant regulatory updates, automated one-click policy updates, and a search tool that lets organizations ensure their employees have the correct state and local payroll withholdings. 
• AI-assisted recruiting tools: Paychex’s Recruiting Copilot lets organizations leverage AI search tools to find and identify talent, send personalized recruiting messages, automate resume screening, and more. 
• General ledger integration with real-time reporting: Through Paychex Flex, you can integrate payroll data with your accounting software through a customizable general ledger that lets you run reports to track costs and assess trends. 

Pricing: CustomPaychex Pricing

10. ADP

Best for: Managing complex, multi-state donor programs 

ADP is an HR and payroll software for nonprofit organizations that need scalable payroll processing across different states. It provides tax filing automation (for both W-2 employees and 1099 contractors), multi-state compliance support services, and tax exemption identification tools. 

With ADP, users can also provide 403(b) retirement plans and benchmark compensation data against competing nonprofits to ensure rates remain competitive. User feedback verifies that the platform is user-friendly and a strong option for simplifying payroll and compliance work, but some point to slow customer service and struggles dealing with complex payroll issues.G2 - ADP Payroll Services Review

Key Features:  

• SmartCompliance® tools: Aggregates disjointed compliance data into one platform with real-time monitoring and provides access to a team of dedicated experts that supports compliance, covering everything from payroll taxes and contractor management to ACA compliance and tax credits. 
• Advanced labor benchmarking against other national nonprofits: Benchmark utilization, compensation, and other key metrics against similar nonprofits through ADP DataCloud, which provides anonymized insights from over a million employers in more than a thousand industries. 
• Integrated 403(b) retirement plans: Set up 403(b) retirement plans for your 501(c)(3) employees with seamless integrations, real-time analytics, a dedicated service team, and more. 

Pricing: CustomADP Payroll Pricing

Features To Look for When Choosing the Best Payroll Software for Nonprofit Organizations 

The best payroll software for nonprofit organizations that offer services made specifically to handle workflows unique to nonprofits. Look for the features below as you build your vendor shortlist. 

Grant-linked labor allocation and fund accounting 

Nonprofit payroll requires tracking labor hours (and other expenses) against specific grants, programs, or restricted funding sources. Your payroll software should let employees tag their time directly at the point of entry and allow administrators to automatically generate audit-ready labor distribution reports for grantors with that data. This saves hours that would otherwise be spent drudging through uncategorized data to build reports manually. 

Integrated volunteer management and valuation 

Nonprofit organizations often handle a variety of worker classifications at any given time, including paid staff (W-2 employees, 1099 contractors) and volunteers. Your nonprofit payroll platform should enable volunteers to track their hours in the same place as your paid staff. This lets organizations calculate the exact value of volunteer time for financial statements and easily administer accurate stipends if necessary. 

Automated Form 990 reporting and tax exemptions 

Automatic federal, state, and local tax compliance for payroll runs is a critical feature for nonprofits, but your platform should also help address more specialized compliance needs. For example, some organizations may qualify for specific tax exemptions (such as a FUTA exemption) or manage workers of varying classifications. As such, your platform of choice should automatically file for those exemptions. It should also feature built-in reporting tools (ideally with AI-powered analytics and insights) to ease the process of filling out the compensation section of IRS Form 990. 

General ledger mapping and accounting integrations 

Modern nonprofit payroll tools should enable organizations to automatically integrate payroll expense data into their primary accounting systems. Your platform of choice should offer native capabilities for general ledger mapping and integrations with industry-standard accounting platforms like QuickBooks and Sage Intacct to eliminate tedious data entry and ensure accuracy across all reports. 

Financial wellness and on-demand pay for staff retention 

In the nonprofit sector, earned wage access (EWA) is often looked at as a competitive benefit. Your platform should let employees access their pay as they earn it through on-demand payments, rather than always waiting for the bi-weekly cycle. This supports your employees' financial stability and can be a powerful tool for mitigating turnover. 

Payroll software for nonprofit organizations FAQs

Here are some answers to common questions about the best nonprofit payroll software.