10 Best Nonprofit Payroll Software in 2026

Nonprofit Payroll Software Reviews

1. 

   1

   Deel Payroll

   Best for global and contractor payroll in one place

   • Free demo available
   • From $29/user/month

   Visit Website

   Customer Rating:4.9/5This rating combines scores from multiple user review sites to reflect overall customer sentiment about the product.

   

   Deel Payroll is a global payroll and contractor management platform that handles multi-country employee payroll, contractor payments, tax filing, and built-in time tracking across 150+ countries.

   Who Is Deel Payroll Best For?

   Deel Payroll is a strong fit for nonprofits that employ a mix of international staff and independent contractors and need both payroll and contractor payments managed in one place.

   Why I Picked Deel Payroll

   I've included Deel Payroll in my top picks because it's the only platform I've found that handles both international employee payroll and contractor payments in one place, which matters for nonprofits running programs across borders with a mix of staff and freelancers. I like that it files 1099-NECs directly from the platform and covers federal, state, and local tax filing across all 50 states automatically. Its percentage-based cost center splits also let you divide wages across programs without manual spreadsheet work.

   Deel Payroll Key Features

   • Built-in time tracking: Workers clock in and out via app, browser, or Slack, with approved hours flowing directly into payroll calculations.
   • Multi-country payroll: Deel processes payroll across 150+ countries in 120+ currencies, covering international staff alongside US employees.
   • Employee self-service portal: Employees can access pay history, year-to-date tax summaries, W-2s, and update direct deposit and withholding details independently.
   • Cost center wage splitting: Wages can be divided across multiple cost centers by percentage with effective dates, supporting labor cost allocation across programs.

   Deel Payroll Integrations

   Deel Payroll offers native GL Sync integrations with QuickBooks Online, Xero, NetSuite, Sage Intacct, SAP, and Microsoft Dynamics. Syncs are manual, and there are no documented integrations with nonprofit platforms such as Aplos or Blackbaud.

   Pros and Cons

   Pros:

   • Supports percentage-based program wage allocation
   • Handles multi-state tax filings automatically
   • Combines employee and contractor payroll

   Cons:

   • Grant reporting remains limited to cost centers
   • No clergy or housing allowance workflows
   Learn more about Deel Payroll:

   • Check out Deel Payroll on their website
2. 

   2

   Workzoom

   Best for coordinating paid staff and volunteers

   • Free demo available
   • From $4/user/month

   Visit Website

   Customer Rating:4.5/5This rating combines scores from multiple user review sites to reflect overall customer sentiment about the product.

   

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   Workzoom is a payroll and HR platform that handles grant-based salary allocation, fund-separated journal entries, volunteer tracking, and multi-jurisdiction pay processing across Canada, the United States, and the Bahamas.

   Who Is Workzoom Best For?

   Workzoom is a strong fit for mid-sized nonprofits with 50 or more employees that need to coordinate paid staff and volunteers within a single payroll and HR system.

   Why I Picked Workzoom

   I picked Workzoom as one of the best because it's one of the few platforms that keeps paid staff and volunteers inside the same scheduling view, so your team isn't toggling between systems to build a shift roster. Where it really shines is grant-based salary allocation: approved hours automatically split across configured grant codes, with fund-separated journal entries generated from those same rules, making funder audit reports far less painful to produce.

   Workzoom Key Features

   • Three-step pay run: Guides payroll through validation, audit and lock, and disbursement, with pre-flight checks that flag missing banking details, unapproved time, and tax-form gaps before processing.
   • Multi-jurisdiction tax calculations: Applies jurisdiction-specific payroll rules across all 50 US states, Canada, and the Bahamas.
   • Volunteer profile tracking: Maintains a distinct profile type for volunteers, separate from paid staff, with hours tracked and excluded from payroll and T4 generation.
   • Statutory payroll outputs: Generates country-specific filing documents, including Canadian T4s and ROEs, US W-2s, and Bahamas NIB outputs, ready for employer review and submission.

   Workzoom Integrations

   Workzoom supports SAML 2.0 single sign-on with Microsoft Entra ID, Okta, and OneLogin. Fund-separated journal entries export as mapped general ledger files for QuickBooks Online and Sage, with Excel export for Power BI and deduction files for benefit carriers. API availability isn’t documented.

   Pros and Cons

   Pros:

   • Reviewers praise responsive implementation support
   • Paid staff and volunteers share scheduling
   • Grant-coded hours generate fund-separated journals

   Cons:

   • Small nonprofits fall below its stated audience
   • Employers submit filings and remit payroll taxes
   Learn more about Workzoom:

   • Check out Workzoom on their website
3. 

   3

   Paylocity

   Best for mid-market grant and program labor tracking

   • Free demo available
   • Pricing upon request

   Visit Website

   Customer Rating:4.3/5This rating combines scores from multiple user review sites to reflect overall customer sentiment about the product.

   

   Paylocity is a unified HR and payroll platform that handles payroll processing, time tracking, tax filing, benefits administration, and labor cost allocation across grants, programs, and funding sources for nonprofit organizations.

   Who Is Paylocity Best For?

   Paylocity is a strong fit for mid-market nonprofits with 100–500 employees that need to track and allocate labor costs across multiple grants, programs, or funding sources.

   Why I Picked Paylocity

   I picked Paylocity as one of the best because of how well it handles labor cost allocation across multiple grants and programs at the timesheet level. Employees can assign hours directly to specific jobs, cost centers, or funding sources, and those hours flow straight into payroll with no duplicate entry. The GL mapping at the payroll code level means finance teams can split a single payroll run across several grant budgets without manual workarounds.

   Paylocity Key Features

   • 403(b) plan administration: Paylocity's built-in retirement module, powered by Vestwell, supports 403(b) plans with automatic payroll-connected contribution syncing.
   • Multi-state payroll processing: Run payroll across all 50 states in a single pay run, with automated state-specific tax calculation, filing, and compliance alerts.
   • Automated tax filing: Paylocity files federal, state, and local taxes—including W-2s, 941s, and 1099s—and assumes liability for any filing errors.
   • Employee self-service mobile app: Employees can access pay stubs, request time off, enroll in benefits, and clock in via the mobile app with biometric and geofencing support.

   Paylocity Integrations

   Paylocity offers native integrations with QuickBooks Online, Sage Intacct, and NetSuite, plus embedded Vestwell retirement administration. Its marketplace includes TrakPay, E-COMP NOW!, SmartPay, Accident Fund, and InsurePay, while APIs support custom integrations.

   Pros and Cons

   Pros:

   • Multi-state tax compliance with real-time alerts
   • Automated housing and clergy payroll settings
   • Handles grant and program labor tracking

   Cons:

   • Limited fund accounting integrations available
   • No nonprofit-specific pricing or discounts
   Learn more about Paylocity:

   • Check out Paylocity on their website
   • Read my in-depth review of Paylocity
   • Explore best alternatives to Paylocity
4. 

   4

   TimeTrex

   Best for time-to-payroll tracking in one place

   • 30-day free trial + free demo available
   • From $50/user/month

   Visit Website

   Customer Rating:4.5/5This rating combines scores from multiple user review sites to reflect overall customer sentiment about the product.

   

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   TimeTrex is a workforce management platform that combines time and attendance tracking, employee scheduling, leave management, and payroll processing in a single system.

   Who Is TimeTrex Best For?

   TimeTrex suits small nonprofits that want time tracking and payroll in one place, particularly those with hourly staff where hours-to-paycheck accuracy matters most.

   Why I Picked TimeTrex

   I picked TimeTrex as one of the best because of how tightly it connects time tracking to payroll, which matters when you're running hourly staff at a nonprofit and need every hour accounted for before a pay run. Clock-in data flows directly into payroll calculations, so there's no manual hour-entry step where numbers can drift. I also like that cost centers can be allocated across up to four levels, letting you tag hours to specific departments or programs before payroll runs.

   TimeTrex Key Features

   • Biometric facial recognition: Employees clock in and out using facial recognition to verify their identity at the point of punch.
   • Leave and absence management: Tracks leave requests, balances, and accruals for paid time off and sick leave in a centralized system.
   • Customizable workforce reports: Generates reports on attendance, labor trends, and payroll data that can be tailored to your organization's needs.
   • QuickBooks and Sage integration: Transfers financial data between TimeTrex and your accounting system via two-way or flat-file data sharing.

   TimeTrex Integrations

   TimeTrex integrations include Intuit QuickBooks, Sage, ADP, Paychex, and Ceridian. It offers a REST API and custom integrations, though nonprofit fund-accounting workflows aren’t specified.

   Pros and Cons

   Pros:

   • Grant-hour summaries support audit preparation
   • Users praise patient, clear support responses
   • Reviewers say time data simplifies payroll runs

   Cons:

   • Customers remain responsible for filing payroll taxes
   • Fund-level payroll allocation isn’t documented
   Learn more about TimeTrex:

   • Check out TimeTrex on their website
5. 

   5

   RUN Powered by ADP®

   Best for small teams with staff across states

   • Free demo available
   • Pricing upon request

   Visit Website

   Customer Rating:4.1/5This rating combines scores from multiple user review sites to reflect overall customer sentiment about the product.

   

   RUN Powered by ADP is a small-business payroll and HR platform that handles payroll processing, payroll tax filing, multi-jurisdiction pay runs, and employee payment disbursement across web, mobile, and phone.

   Who Is RUN Powered by ADP Best For?

   RUN Powered by ADP is a strong fit for small nonprofits with payroll administrators who need reliable multi-state tax filing and payment disbursement without managing compliance manually.

   Why I Picked RUN Powered by ADP

   I picked RUN Powered by ADP as one of the best because it handles multi-jurisdiction payroll within a single pay period, with ADP managing the associated tax filing automatically. For small nonprofits with staff spread across state lines, that means no manually tracking which state taxes apply to which employee. I also like the Tax Notices feature, which lets you photograph a tax agency notice and hand it directly to ADP's tax team to resolve.

   RUN Powered by ADP Key Features

   • Automated payroll tax filing: RUN calculates, deposits, and reconciles payroll taxes across federal, state, and local jurisdictions, with ADP handling tax agency inquiries directly.
   • ADP Assist payroll inspector: An AI-enabled tool flags potential payroll errors before you submit, giving you a chance to correct mistakes in the preview stage.
   • State Unemployment Insurance management: Available on Enhanced Payroll and above, this feature audits SUI experience rates and handles state agency correspondence on your behalf.
   • General ledger interface: Exports payroll journal entries to QuickBooks, Xero, Wave, or Creative Solutions after each pay run.

   RUN Powered by ADP Integrations

   RUN Powered by ADP offers native integrations with QuickBooks, Xero, Wave, and Creative Solutions, plus a 7shifts marketplace integration and an API for custom integrations.

   Pros and Cons

   Pros:

   • Handles employees across multiple tax jurisdictions
   • Automated tax filing reduces manual compliance work
   • Reviewers praise quick payroll runs

   Cons:

   • No documented clergy-specific payroll handling
   • Department coding doesn’t track grants or funds
   Learn more about RUN Powered by ADP®:

   • Check out RUN Powered by ADP® on their website
   • Read my in-depth review of RUN Powered by ADP®
6. 

   6

   Netchex

   Best for clergy and grant-funded payroll

   • Free demo available
   • Pricing upon request

   Visit Website

   Customer Rating:4.5/5This rating combines scores from multiple user review sites to reflect overall customer sentiment about the product.

   

   Netchex is a full-service payroll and HR platform built for nonprofits, handling payroll processing, tax filing, time tracking, fund and grant allocation, and benefits administration in one system.

   Who Is Netchex Best For?

   Netchex is a strong fit for mid-sized nonprofits and faith-based organizations that need clergy payroll, housing allowance tracking, and multi-grant labor cost allocation handled natively in one platform.

   Why I Picked Netchex

   Netchex earns its spot on my shortlist because it handles clergy payroll and grant-funded labor allocation as native platform features, not manual workarounds. I particularly like how it supports minister dual-status payroll, IRC §107 housing allowance tracking with W-2 annotation, and Form 4361 Social Security opt-outs configured directly in the system. On the grant side, you can split a single employee's labor costs across multiple funds and programs at the timecard level, which flows automatically into audit-ready reporting.

   Netchex Key Features

   • OneScreen Payroll™ dashboard: Aggregates payroll readiness data across multiple locations or entities so you can review and run payroll in a single view.
   • ACT Verification tool: Automatically checks that each employee is taxed correctly based on their work location, covering all 50 states.
   • Timecard-level job code tracking: Links time entries to specific departments, cost centers, and programs directly on the timecard before payroll processes.
   • AI anomaly monitoring via Sentinel: Continuously scans payroll data for compliance issues, approval errors, and compensation changes between pay periods.

   Netchex Integrations

   Netchex documents 23+ accounting and GL integrations, including QuickBooks Online, Blackbaud Financial Edge, MIP, Sage 50, Sage 300, Oracle NetSuite, and Microsoft Dynamics 365 Business Central. It also lists 44+ 401(k) provider integrations and supports custom GL file formats.

   Pros and Cons

   Pros:

   • ACA, SUI, WOTC, and 501(c)(3) compliance
   • Audit-ready fund and grant allocation built-in
   • Clergy payroll and housing allowance automated

   Cons:

   • Interface slow and cumbersome for small teams
   • No clear support for 403(b) plans
   Learn more about Netchex:

   • Check out Netchex on their website
7. 

   7

   UKG Ready

   Best for grant labor allocation at payroll

   • Free demo available
   • Pricing upon request

   Visit Website

   Customer Rating:4.4/5This rating combines scores from multiple user review sites to reflect overall customer sentiment about the product.

   

   UKG Ready is an HR and payroll platform with built-in time tracking, benefits administration, tax filing, and grant labor allocation tools designed for mid-to-large nonprofit organizations.

   Who Is UKG Ready Best For?

   UKG Ready is a strong fit for mid-to-large nonprofits that manage grant-funded programs and need payroll to reflect real-time labor allocations across multiple funding sources.

   Why I Picked UKG Ready

   I picked UKG Ready as one of the best because its dedicated "Time and Effort Reporting for Grants" module does something most payroll platforms don't: it lets you assign labor costs to specific grants in real time, with dashboards showing live spend versus budget. You can set employee rates by grant, track hours against milestones, and run role-based timesheet approvals that distinguish between, say, a principal investigator and a program assistant. Native 403(b) administration with 15-year rule support rounds out the nonprofit fit.

   UKG Ready Key Features

   • SmartCheck™ payroll error flagging: An AI-powered review scans each payroll run and surfaces potential errors before you finalize it.
   • Multi-EIN payroll support: Run payroll across separate chapters, campuses, or affiliated entities under a single platform login.
   • 403(b) catch-up contribution administration: Native setup supports 15-year rule provisions and USERRA make-up contributions for nonprofit retirement plans.
   • Automated multi-jurisdiction tax filing: Federal, state, and local tax submissions—including W-2s, 1099s, and 941s—are filed end-to-end on your behalf.

   UKG Ready Integrations

   UKG Ready has documented integrations with QuickBooks and NetSuite, plus a Sage Intacct Marketplace connection. These accounting integrations support payroll-to-ledger workflows for nonprofit finance teams.

   Pros and Cons

   Pros:

   • Multi-entity payroll under one login
   • Native 403(b) 15-year rule support
   • Real-time grant labor allocation during payroll

   Cons:

   • Reporting tools require administrative expertise
   • No pre-built clergy tax workflows
   Learn more about UKG Ready:

   • Check out UKG Ready on their website
   • Read my in-depth review of UKG Ready
8. 

   8

   Apspayroll

   Best for grant and fund labor cost allocation

   • Free demo available
   • From $6/user/month

   Visit Website

   

   APS Payroll is a payroll and HR platform built with dedicated support for nonprofits and faith-based organizations, covering payroll processing, tax compliance, time tracking, benefits administration, and grant-level labor cost allocation.

   Who Is APS Payroll Best For?

   APS Payroll is a strong fit for nonprofits and faith-based organizations that need to allocate labor costs across multiple grants or programs and want a dedicated support team.

   Why I Picked APS Payroll

   APS Payroll earns its spot on my shortlist because of its Dimensions module, which lets you tag employee time directly to specific grants, programs, or departments at the timecard level. I love that those allocations flow straight into payroll processing and GL exports, so there's no manual rework when you're reconciling labor costs across multiple funding sources. The platform also handles 501(c)(3) FUTA exemptions and clergy dual-status taxation natively, which matters if your organization runs a mixed workforce of lay staff and ordained ministers.

   APS Payroll Key Features

   • Clergy housing allowance tracking: Set up, document, and track ministerial housing allowances to support correct federal income tax exclusion treatment.
   • Employee self-service portal: Staff can view pay stubs, update direct deposit details, adjust W-4 withholding, and request time off through a web or mobile app.
   • Sage Intacct bidirectional integration: Syncs employee records and dimensions between APS and Sage Intacct, then automatically posts payroll GL data by dimension into your fund accounting system.
   • Custom report builder: Build ad hoc payroll and labor expense reports using configurable filters and columns to support board presentations and Form 990 preparation.

   APS Payroll Integrations

   APS Payroll lists 238 total connections, including a native bidirectional Sage Intacct integration plus integrations with QuickBooks, AccountMate, Acumatica, ACS Technologies, and Employee Navigator. An open API supports custom integrations.

   Pros and Cons

   Pros:

   • Handles clergy housing allowance and dual-status
   • Dedicated nonprofit and faith-based support teams
   • Grant-level labor cost allocation with audit trails

   Cons:

   • No Aplos or Blackbaud Financial Edge NXT integration
   • High monthly minimum excludes small nonprofits
   Learn more about Apspayroll:

   • Check out Apspayroll on their website
9. 

   9

   UKG Inova Payroll

   Best for clergy and grant-level payroll compliance

   • Free demo available
   • Pricing upon request

   Visit Website

   

   UKG Inova Payroll is a full-service payroll platform built for nonprofits, handling automated payroll processing, multi-state tax filing, clergy housing allowances, grant-level labor cost allocation, and fund accounting integrations across organizations of all sizes.

   Who Is UKG Inova Payroll Best For?

   UKG Inova Payroll is a strong fit for faith-based organizations and nonprofits managing federally funded programs that need clergy housing allowance support and grant-level labor cost tracking in one payroll system.

   Why I Picked UKG Inova Payroll

   I've included UKG Inova Payroll in my top picks because it handles two of the most technically demanding nonprofit payroll scenarios out of the box: clergy compensation and grant-level labor tracking. I specifically like that it supports housing allowances, Form 4361, and minister dual-status configuration, which most generalist platforms simply don't address. On the grant side, you can code timecards directly to funding sources, set primary and secondary funding splits per employee, and pull grant-level labor reports that hold up to OMB Uniform Guidance requirements.

   UKG Inova Payroll Key Features

   • Full-service tax filing: Files Forms 940, 941, 944, W-2, W-3, and 1099 across all 50 states and Washington, D.C., with automated reciprocity withholding and geospatial local tax ID matching.
   • Multi-EIN payroll management: Manages payroll across multiple affiliated entities, chapters, or campuses under one login with separate EIN handling and consolidated reporting.
   • Pay-as-you-go workers' comp: Calculates workers' compensation premiums per payroll run with no down payment, avoiding large year-end true-ups.
   • Sage Intacct integration: Syncs payroll data bidirectionally with Sage Intacct, auto-posting GL journal entries by department, location, and dimension after each payroll run.

   UKG Inova Payroll Integrations

   UKG Inova Payroll integrates with Sage Intacct, QuickBooks Online, Acumatica, and Xero. It also provides an open REST API for custom connections, while Sage Intacct supports bidirectional GL and dimension syncing.

   Pros and Cons

   Pros:

   • Manages multi-EIN nonprofit payroll compliance
   • Supports grant-level labor cost tracking
   • Handles clergy housing and parsonage allowances

   Cons:

   • No free trial or instant sandbox access
   • No explicit support for 403(b) retirement plans
   Learn more about UKG Inova Payroll:

   • Check out UKG Inova Payroll on their website
10. 

    10

    Payroll Partners

    Best for church and clergy payroll compliance

    • Not available
    • Pricing upon request

    Visit Website

    

    Payroll Partners is a payroll and HR platform built specifically for churches and faith-based nonprofits, covering clergy tax handling, multi-campus labor allocation, time and attendance, benefits enrollment, and ATS-integrated recruiting.

    Who Is Payroll Partners Best For?

    Payroll Partners is built for churches and faith-based nonprofits that need clergy housing allowance management, dual-status minister tax handling, and multi-campus payroll support in one place.

    Why I Picked Payroll Partners

    Payroll Partners earns its spot on my shortlist because no other platform handles clergy payroll complexity with this level of specificity. I'm particularly impressed by its dual-status minister tax handling, which correctly separates FICA from SECA obligations, and its dedicated clergy housing allowance workflows, which even support mid-year reviews when a pastor's expenses change. It also manages pay confidentiality for pastoral staff, something most general payroll platforms simply don't offer.

    Payroll Partners Key Features

    • ATS-integrated recruiting: Post open roles directly to Indeed, Glassdoor, and ZipRecruiter, then manage candidate prescreening, scoring, and committee review workflows within the same platform.
    • Paperless onboarding: New hires complete offer letter signing, federal and state forms, and I-9 verification online, with manager and employee task checklists tracking each step.
    • ACA compliance dashboard: Tracks Applicable Large Employer status, generates 1094-C and 1095-C forms, and handles electronic filing with built-in compliance alerts.
    • Multi-method time tracking: Employees can clock in via physical time clocks (badge, biometric, or proximity fob), web portal timesheets, or mobile app, with hours feeding directly into payroll.

    Payroll Partners Integrations

    Payroll Partners integrates with QuickBooks, Sage, Shelby Systems, Blackbaud, and ACS for accounting workflows. It also connects with Indeed, Glassdoor, and ZipRecruiter through its ATS, with custom integrations available on request.

    Pros and Cons

    Pros:

    • Dedicated multi-campus labor allocation features
    • Dual-status minister tax workflows included
    • Handles clergy housing and parsonage allowances

    Cons:

    • Employee portal interface feels dated
    • No public pricing or trial available
    Learn more about Payroll Partners:

    • Check out Payroll Partners on their website