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Payroll and Benefits Platforms for Nonprofits and Associations
Albert Richer

Navigating the Best Payroll and Benefits Platforms for Nonprofits and Associations: Insights from Market Analysis When analyzing customer feedback across multiple platforms, it's clear that nonprofits and associations prioritize affordability and ease of use in payroll and benefits software. Market research indicates that solutions like Gusto and Paychex frequently appear in top-rated lists, largely due to their user-friendly interfaces and robust customer support. However, many organizations often overthink the importance of features like advanced reporting tools, which, while valuable, may not be as critical as straightforward payroll processing for smaller teams. Data suggests that Gusto is often praised for its intuitive design, making payroll processing feel less like rocket science—perfect for organizations with limited tech-savvy staff. In contrast, reviews indicate that Paychex shines in scalability, which may help growing nonprofits handle fluctuating employee counts without a hitch. But do we really need a dashboard that looks like the cockpit of a spaceship? Navigating the Best Payroll and Benefits Platforms for Nonprofits and Associations: Insights from Market Analysis When analyzing customer feedback across multiple platforms, it's clear that nonprofits and associations prioritize affordability and ease of use in payroll and benefits software.

Similar Categories
1
Expert Score
9.8 / 10
384
145

Netchex Non-Profit HR & Payroll

Netchex Non-Profit HR & Payroll
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Netchex is a comprehensive SaaS solution designed for non-profits, addressing their unique needs such as complex benefits eligibility, efficient recruiting, onboarding, and accurate payroll processing. Its integrated HR and Payroll functionalities simplify tax management, making it an ideal solution for this specific industry.
Netchex is a comprehensive SaaS solution designed for non-profits, addressing their unique needs such as complex benefits eligibility, efficient recruiting, onboarding, and accurate payroll processing. Its integrated HR and Payroll functionalities simplify tax management, making it an ideal solution for this specific industry.

Best for teams that are

  • Mid-sized nonprofits needing a unified HR and payroll platform
  • Organizations with multiple locations or divisions
  • Nonprofits wanting a balance of technology and service support

Skip if

  • Very small nonprofits with simple payroll structures
  • Organizations requiring complex benefits administration or deep integrations
  • Users needing a highly scalable enterprise-level solution

Expert Take

Netchex is specifically tailored to non-profits, providing solutions to unique challenges in this sector. The software provides efficient recruiting and onboarding, simplifies tax management, and offers accurate payroll processing. Its ability to handle complex benefit eligibility sets it apart, making it a go-to solution for non-profits. The integrated HR and payroll features streamline operations, saving time and resources for organizations that may have limited staff and budgets.

Pros

  • Integrated HR and Payroll features
  • Efficient recruiting and onboarding
  • Simplified tax management
  • Accurate payroll processing
  • Complex benefits eligibility management

Cons

  • No free plan
  • May require some learning curve for non-tech savvy users
2
Expert Score
9.7 / 10
552
74
EXCEPTIONAL SUPPORT
GRANT-FRIENDLY

SurePayroll Nonprofit Services

SurePayroll Nonprofit Services
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SurePayroll is designed specifically to address the unique payroll needs of nonprofit organizations. It simplifies payroll processes with features like W-2, 1099 tax filings, and direct deposits. It caters to the industry with its stress-free, accurate, and reliable payroll services that free up time for nonprofits to focus on their mission.
SurePayroll is designed specifically to address the unique payroll needs of nonprofit organizations. It simplifies payroll processes with features like W-2, 1099 tax filings, and direct deposits. It caters to the industry with its stress-free, accurate, and reliable payroll services that free up time for nonprofits to focus on their mission.
EXCEPTIONAL SUPPORT
GRANT-FRIENDLY

Best for teams that are

  • Small nonprofits and micro-organizations with simple payroll needs
  • Budget-conscious organizations needing affordable, full-service payroll
  • Nonprofits needing specific support for clergy housing allowances

Skip if

  • Growing nonprofits that will quickly outgrow basic features
  • Organizations requiring advanced time-off management or 24/7 support
  • Users needing complex grant tracking or labor distribution

Expert Take

SurePayroll stands out because it addresses the unique payroll needs of nonprofits, a sector often overlooked by traditional payroll services. It simplifies complex payroll processes, ensuring tax compliance and accurate direct deposits. This allows nonprofit professionals to focus on their mission rather than administrative tasks. The platform's ease of use and dedicated customer support also make it a reliable choice for nonprofits.

Pros

  • Easy-to-use interface
  • Comprehensive tax filing services
  • Reliable direct deposit feature
  • Specialized for nonprofits
  • Outstanding customer support

Cons

  • Pricing isn’t transparent
  • No free trial offered
  • May be too feature-rich for smaller nonprofits
3
Expert Score
9.6 / 10
660
150
MISSION FOCUSED
ALL-IN-ONE PLATFORMS

Paycom HR & Payroll

Paycom HR & Payroll
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Paycom offers a comprehensive, all-in-one HR and payroll software solution specifically tailored for nonprofit organizations. It streamlines employee processes, automates repetitive tasks, and ensures compliance with labor laws, helping nonprofits to focus more on their mission.
Paycom offers a comprehensive, all-in-one HR and payroll software solution specifically tailored for nonprofit organizations. It streamlines employee processes, automates repetitive tasks, and ensures compliance with labor laws, helping nonprofits to focus more on their mission.
MISSION FOCUSED
ALL-IN-ONE PLATFORMS

Best for teams that are

  • Mid-sized to large nonprofits prioritizing a single-database system
  • Organizations wanting to empower employees with self-service payroll (Beti)
  • Nonprofits needing strict data integrity without third-party integrations

Skip if

  • Small nonprofits with limited budgets due to high cost and complexity
  • Organizations requiring global payroll capabilities
  • Users who prefer a hands-off payroll process over employee-driven verification

Expert Take

Paycom stands out for its unique understanding of the nonprofit sector. Its software not only automates HR and payroll tasks, but it also incorporates features that are specific to the needs of nonprofits such as donor management and volunteer coordination. This software is loved by industry professionals for its capacity to alleviate administrative burdens, allowing nonprofits to focus more on their mission and impact.

Pros

  • Nonprofit-specific features
  • Automates HR tasks
  • Guarantees compliance
  • All-in-one platform
  • 24/7 support

Cons

  • Steep learning curve
  • No free plan
  • Might be expensive for small nonprofits
4
Expert Score
9.6 / 10
686
156
DATA SECURITY CHAMPS

Paylocity for Nonprofits

Paylocity for Nonprofits
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Paylocity is an all-in-one HR and payroll software solution tailored to meet the unique needs of nonprofits and 501c3 organizations. This platform automates essential HR tasks, allowing organizations to focus more on their mission, while ensuring efficient payroll and benefits administration.
Paylocity is an all-in-one HR and payroll software solution tailored to meet the unique needs of nonprofits and 501c3 organizations. This platform automates essential HR tasks, allowing organizations to focus more on their mission, while ensuring efficient payroll and benefits administration.
DATA SECURITY CHAMPS

Best for teams that are

  • Mid-sized to large nonprofits needing volunteer tracking and engagement tools
  • Organizations requiring detailed grant tracking and labor allocation
  • Nonprofits focusing on community and social collaboration features

Skip if

  • Small nonprofits with fewer than 50 employees due to complexity and cost
  • Organizations preferring a single database architecture over integrated modules
  • Users wanting transparent, published pricing without sales quotes

Expert Take

Our analysis shows Paylocity distinguishes itself in the nonprofit sector by directly addressing the complex burden of fund accounting. Unlike generic payroll providers, Paylocity includes built-in tools for grant tracking and labor allocation that flow directly into Form 990 reporting. Furthermore, its documented integration with Blackbaud Financial Edge NXT creates a seamless bridge between payroll and the industry-standard nonprofit ERP. While support consistency remains a documented challenge, the platform's specialized compliance features offer significant value for mission-driven organizations.

Pros

  • Grant tracking & labor allocation
  • Blackbaud Financial Edge integration
  • Automated Form 990 reporting
  • 92%+ revenue retention rate
  • Mobile-first employee self-service

Cons

  • Inconsistent customer support quality
  • Opaque pricing structure
  • Implementation can be complex
  • High turnover of account managers
  • Extra fees for add-on modules
5
Expert Score
9.3 / 10
640
121

PSS Nonprofit Payroll

PSS Nonprofit Payroll
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PSS Nonprofit Payroll is a specifically tailored solution for nonprofit organizations. It addresses the unique financial and HR needs of nonprofits, ensuring accurate payroll processing, tax compliance, and benefits administration.
PSS Nonprofit Payroll is a specifically tailored solution for nonprofit organizations. It addresses the unique financial and HR needs of nonprofits, ensuring accurate payroll processing, tax compliance, and benefits administration.

Best for teams that are

  • Small to mid-sized nonprofits seeking personalized, hands-on support
  • Organizations specifically needing assistance with FUTA exemptions
  • Nonprofits preferring a regional partner with a personal touch

Skip if

  • Large enterprises requiring advanced, automated HCM software suites
  • Users preferring a fully automated, self-service DIY platform
  • Organizations needing global payroll support

Expert Take

PSS Nonprofit Payroll stands out for its nonprofit-centric approach. It understands the financial constraints and compliance pressures that nonprofits face. With this software, nonprofits can automate their payroll processes, ensuring accurate, timely payments and tax deductions. Its dedicated customer support is also a major plus, providing timely assistance to address any issues or queries.

Pros

  • Specialized for nonprofits
  • Streamlines payroll processes
  • Ensures tax compliance
  • Assists in benefits administration
  • Dedicated customer support

Cons

  • Pricing not transparent
  • Requires contact for demo
  • May not integrate with all HR systems
6
Expert Score
9.3 / 10
468
82
SEAMLESS INTEGRATIONS
RAPID PAYROLL

OnPay Nonprofit Payroll Software

OnPay Nonprofit Payroll Software
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OnPay's Nonprofit Payroll Software is a tailored solution for 501(c)(3) charities, providing fast and efficient payroll processing for both employees and contractors. The software understands the unique financial and administrative challenges faced by charitable organizations, and is equipped with industry-specific features to meet these needs.
OnPay's Nonprofit Payroll Software is a tailored solution for 501(c)(3) charities, providing fast and efficient payroll processing for both employees and contractors. The software understands the unique financial and administrative challenges faced by charitable organizations, and is equipped with industry-specific features to meet these needs.
SEAMLESS INTEGRATIONS
RAPID PAYROLL

Best for teams that are

  • Small to mid-sized nonprofits needing affordable, flat-rate pricing
  • Organizations requiring automated 501(c)(3) tax exemptions and clergy payroll
  • Nonprofits needing unlimited pay runs for grant-based labor distribution

Skip if

  • Large enterprises requiring advanced HCM or global payroll capabilities
  • Users who prioritize a native mobile app for employer administration
  • Organizations needing built-in time and attendance hardware

Expert Take

Our analysis shows OnPay is uniquely optimized for the nonprofit sector, automating complex tasks like 501(c)(3) FUTA exemptions and clergy housing allowances that generalist providers often miss. Research indicates the pricing model is exceptionally transparent, with a single tier that includes multi-state processing and HR tools, avoiding the hidden costs found in competitor 'enterprise' plans. Based on documented TechSoup partnerships, the six-month free offer provides significant value for budget-conscious organizations.

Pros

  • Automates 501(c)(3) FUTA exemptions
  • Supports clergy housing allowances
  • Transparent single-tier pricing
  • 6 months free via TechSoup
  • Unlimited monthly pay runs

Cons

  • No native employer mobile app
  • No built-in time tracking
  • Limited third-party integrations
  • Support not 24/7
  • Manual grant tracking setup
7
Expert Score
9.0 / 10
605
161
COST SAVERS

ADP Nonprofit Payroll & HR

ADP Nonprofit Payroll & HR
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The ADP Nonprofit Payroll & HR software is designed to cater to the unique needs of 501(c)(3) organizations. It offers essential tools to help control costs, meet compliance obligations, and empower staff, which are critical for any nonprofit. Additionally, it nurtures connections to promote efficient operations within the organization.
The ADP Nonprofit Payroll & HR software is designed to cater to the unique needs of 501(c)(3) organizations. It offers essential tools to help control costs, meet compliance obligations, and empower staff, which are critical for any nonprofit. Additionally, it nurtures connections to promote efficient operations within the organization.
COST SAVERS

Best for teams that are

  • Mid-sized to large nonprofits needing scalable compliance and grant tracking
  • Organizations requiring robust labor distribution for multiple funding sources
  • Nonprofits needing 24/7 support and deep regulatory expertise

Skip if

  • Very small teams with simple needs and tight budgets
  • Organizations preferring transparent, non-quote-based pricing models
  • Users wanting a simple, low-learning-curve interface

Expert Take

ADP's Nonprofit Payroll & HR solution is a one-stop-shop for nonprofits, offering features that address the specific challenges in the sector. Compliance, a major concern for nonprofits, is made easier with automated tools. It's a comprehensive solution that empowers employees, manages costs, and enhances connections — all essential elements for the smooth operation of a nonprofit.

Pros

  • Industry-specific features
  • Automated compliance tools
  • Efficient people management
  • Cost control tools

Cons

  • Requires time to fully understand
  • Pricing isn't transparent
  • Features may be overwhelming for small nonprofits
8
Expert Score
8.9 / 10
694
61
TAILORED SOLUTIONS
BENEFITS MASTERY

Paychex HR & Payroll for Nonprofits

Paychex HR & Payroll for Nonprofits
View Website
Paychex offers a comprehensive HR and payroll platform designed specifically for nonprofits, helping them stay compliant, efficient, and mission-focused. The solution is tailored to address the unique payroll, HR, and benefits challenges faced by nonprofit organizations, such as managing complex grant and fund accounting, ensuring regulatory compliance, and attracting and retaining talent.
Paychex offers a comprehensive HR and payroll platform designed specifically for nonprofits, helping them stay compliant, efficient, and mission-focused. The solution is tailored to address the unique payroll, HR, and benefits challenges faced by nonprofit organizations, such as managing complex grant and fund accounting, ensuring regulatory compliance, and attracting and retaining talent.
TAILORED SOLUTIONS
BENEFITS MASTERY

Best for teams that are

  • Larger nonprofits requiring dedicated support specialists and complex HR tools
  • Organizations needing integrated 401(k) and benefits administration
  • Nonprofits needing assistance with complex tax credit services

Skip if

  • Small nonprofits seeking the lowest cost or DIY payroll solutions
  • Users wanting to avoid potential add-on fees for basic features
  • Organizations preferring a purely software-focused self-service model

Expert Take

Our analysis shows that Paychex stands out for nonprofits primarily due to its robust labor distribution capabilities, which are essential for organizations managing multiple grants and funding sources. Research indicates that its seamless integration with nonprofit-favored accounting platforms like Sage Intacct allows for precise general ledger mapping, significantly reducing administrative burden during audits. While pricing transparency is a noted limitation, the depth of compliance features makes it a strong contender for established nonprofits.

Pros

  • Automated labor distribution for grants
  • Integrates with Sage Intacct & QuickBooks
  • Highly rated mobile app (4.8/5)
  • Scalable for growing organizations
  • Comprehensive tax compliance services

Cons

  • Pricing is not publicly transparent
  • Potential hidden 401(k) fees
  • Desktop interface described as dated
  • Support quality varies by representative
  • Add-on modules increase total cost

Product Comparison

Product Has Mobile App Has Free Plan Has Free Trial Integrates With Zapier Has Public API Live Chat Support SOC 2 or ISO Certified Popular Integrations Supports SSO Starting Price
1 Netchex Non-Profit HR & Payroll
Yes No Contact for trial Yes Yes Yes SOC 2 QuickBooks, ADP, Microsoft 365 Yes Enterprise pricing
2 SurePayroll Nonprofit Services
Yes No No No No Yes Not specified QuickBooks, Xero, Intuit No Custom pricing
3 Paycom HR & Payroll
Yes No Contact for trial No Enterprise API only Yes SOC 2 QuickBooks, Salesforce, Microsoft 365 Yes Enterprise pricing
4 Paylocity for Nonprofits
Yes No Contact for trial Yes Yes Yes SOC 2 Slack, Microsoft Teams, Google Workspace Yes Enterprise pricing
5 PSS Nonprofit Payroll
No No Contact for trial No No Email/Ticket only Not specified Limited integrations No Custom pricing
6 OnPay Nonprofit Payroll Software
Yes No Yes - 30 days Yes Yes Yes Not specified QuickBooks, Xero, TSheets No $36/month plus $4 per person
7 ADP Nonprofit Payroll & HR
Yes No Contact for trial No Enterprise API only Yes SOC 2 QuickBooks, Salesforce, Microsoft 365 Yes Custom pricing
8 Paychex HR & Payroll for Nonprofits
Yes No Contact for trial Yes Yes Yes SOC 2 QuickBooks, Xero, Indeed Yes Custom pricing
1

Netchex Non-Profit HR & Payroll

Has Mobile App
Yes
Has Free Plan
No
Has Free Trial
Contact for trial
Integrates With Zapier
Yes
Has Public API
Yes
Live Chat Support
Yes
SOC 2 or ISO Certified
SOC 2
Popular Integrations
QuickBooks, ADP, Microsoft 365
Supports SSO
Yes
Starting Price
Enterprise pricing
2

SurePayroll Nonprofit Services

Has Mobile App
Yes
Has Free Plan
No
Has Free Trial
No
Integrates With Zapier
No
Has Public API
No
Live Chat Support
Yes
SOC 2 or ISO Certified
Not specified
Popular Integrations
QuickBooks, Xero, Intuit
Supports SSO
No
Starting Price
Custom pricing
3

Paycom HR & Payroll

Has Mobile App
Yes
Has Free Plan
No
Has Free Trial
Contact for trial
Integrates With Zapier
No
Has Public API
Enterprise API only
Live Chat Support
Yes
SOC 2 or ISO Certified
SOC 2
Popular Integrations
QuickBooks, Salesforce, Microsoft 365
Supports SSO
Yes
Starting Price
Enterprise pricing
4

Paylocity for Nonprofits

Has Mobile App
Yes
Has Free Plan
No
Has Free Trial
Contact for trial
Integrates With Zapier
Yes
Has Public API
Yes
Live Chat Support
Yes
SOC 2 or ISO Certified
SOC 2
Popular Integrations
Slack, Microsoft Teams, Google Workspace
Supports SSO
Yes
Starting Price
Enterprise pricing
5

PSS Nonprofit Payroll

Has Mobile App
No
Has Free Plan
No
Has Free Trial
Contact for trial
Integrates With Zapier
No
Has Public API
No
Live Chat Support
Email/Ticket only
SOC 2 or ISO Certified
Not specified
Popular Integrations
Limited integrations
Supports SSO
No
Starting Price
Custom pricing
6

OnPay Nonprofit Payroll Software

Has Mobile App
Yes
Has Free Plan
No
Has Free Trial
Yes - 30 days
Integrates With Zapier
Yes
Has Public API
Yes
Live Chat Support
Yes
SOC 2 or ISO Certified
Not specified
Popular Integrations
QuickBooks, Xero, TSheets
Supports SSO
No
Starting Price
$36/month plus $4 per person
7

ADP Nonprofit Payroll & HR

Has Mobile App
Yes
Has Free Plan
No
Has Free Trial
Contact for trial
Integrates With Zapier
No
Has Public API
Enterprise API only
Live Chat Support
Yes
SOC 2 or ISO Certified
SOC 2
Popular Integrations
QuickBooks, Salesforce, Microsoft 365
Supports SSO
Yes
Starting Price
Custom pricing
8

Paychex HR & Payroll for Nonprofits

Has Mobile App
Yes
Has Free Plan
No
Has Free Trial
Contact for trial
Integrates With Zapier
Yes
Has Public API
Yes
Live Chat Support
Yes
SOC 2 or ISO Certified
SOC 2
Popular Integrations
QuickBooks, Xero, Indeed
Supports SSO
Yes
Starting Price
Custom pricing

Similar Categories

How We Rank Products

Our Evaluation Process

In the evaluation of payroll and benefits platforms for nonprofits and associations, key factors considered include product specifications, features, customer reviews, and overall ratings. Specific considerations important to this category include compliance with nonprofit regulations, user-friendly interfaces, and scalable solutions that cater to the unique needs of nonprofit organizations. The research methodology focuses on a thorough analysis of product specifications, comparative research of customer feedback, and an evaluation of the price-to-value ratio to determine the rankings of the ten selected products. This comprehensive approach ensures that the most relevant and impactful platforms are identified for organizations seeking efficient payroll and benefits solutions.

Overall scores reflect relative ranking within this category, accounting for which limitations materially affect real-world use cases. Small differences in category scores can result in larger ranking separation when those differences affect the most common or highest-impact workflows.

Verification

  • Products evaluated through comprehensive research and analysis of nonprofit payroll and benefits features.
  • Rankings based on analysis of user reviews, expert ratings, and industry benchmarks.
  • Selection criteria focus on compliance, affordability, and user satisfaction in payroll and benefits solutions for nonprofits.

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Score Breakdown

0.0 / 10

What This Award Means