Nonprofit organizations operate with unique financial and regulatory constraints that make managing payroll especially demanding. From dealing with grant-funded positions and tax-exempt status to compensating a mix of employees and volunteers, HR teams often face complex challenges that typical payroll software aren’t equipped to handle.

To help with this issue, businesses often make use of payroll software that’s tailored for nonprofits. These systems get rid of all kinds of payroll headaches by automating compliance, accurately allocating funds, and simplifying tax reporting. With the right tools in place, nonprofits can reduce errors, save time, and dedicate more energy to their core mission.

All that said, you might be wondering where to start. Don’t fret though—we’ve come up with a list of the 7 best payroll solutions that are geared to meet the needs of various nonprofit organizations.

Top 7 Payroll Software For Nonprofit Organizations

Company 

Best for

Main Features 

Pricing

Gusto

Streamlining payroll

  • Automatically files taxes
  • Built-in time tracking
  • Integrations with nonprofit accounting systems

Starts at $49/month

ADP

Growing nonprofit organizations 

  • In-built marketplace for integrations
  • Flexible payment options for employees
  • Provides analytics to improve retention

Customized pricing

Paycom

Onboarding and employee training

  • Error free payroll
  • Thorough background checks
  • Flexible learning management system

Customized pricing 

BambooHR 

Employee experience

  • Customizable employee database
  • Detailed reporting tools
  • Mobile App
  •   

Customized pricing

Paylocity

Workforce engagement

  • Accurate payroll processing
  • Employee self-service portal
  • Employee recognition tools

Customized pricing

Paycor

Maintaining compliance

  • Grants access to tax experts
  • Real-time workforce analytics
  • Fully branded career sites

Customized pricing

Justworks

Small nonprofits

  • Full-service payroll with automated tax filings
  • Access to benefits typically reserved for larger organizations
  • HR support and compliance guidance

Starting from $8/month/employee

Gusto – Best For Streamlining Payroll

Gusto HR Software offers an intuitive payroll and HR platform that can also be used by nonprofits. It helps simplify back-office operations by automating payroll, tax filings, and benefits management, while supporting compliance with federal, state, and nonprofit-specific regulations. Designed for all kinds of companies, Gusto also supports time tracking, onboarding, and contractor payments through a single platform.

Standout Features

  • Automated tax filing: Automatically files federal, state, and local payroll taxes, reducing compliance risks for nonprofit organizations.
  • Built-in time tracking: Offers built-in time tracking as well as time-off requests.
  • Accounting integrations: Provides integrations with nonprofit accounting systems like Aplos and MonkeyPod.

Pricing

Gusto offers multiple plans starting at $49/month plus $6/month/person. Discounts may be available for qualifying nonprofit organizations.

Disclaimer: The pricing is subject to change.

Why Choose Gusto

Gusto is ideal for nonprofit organizations looking for a user-friendly, all-in-one payroll and HR platform that reduces administrative time and ensures compliance. It’s especially valuable for smaller teams managing diverse roles and funding sources without a dedicated HR department.

ADP – Best For Growing Nonprofits

ADP Workforce Now provides an extensive payroll and HR services tailored for nonprofit and social service organizations of all sizes. With its scalable solutions, ADP supports everything from small community groups to large, multi-location nonprofits. It also offers automated payroll, tax filing, and time tracking—along with strategic HR support to help nonprofits manage compliance, reduce risk, and optimize staffing.

Standout Features

  • Includes an in-built marketplace for third-party HR software integrations.
  • Provides flexible payment options for employees, such as paperless pay through systems like Wisely.
  • Offers workforce analytics, talent management, and other HR tools to help nonprofits improve operations and staff retention.

Pricing

ADP’s pricing is customized based on organizational size and services required.

Disclaimer: The pricing is subject to change.

Why Choose ADP

ADP is an excellent fit for nonprofits looking for long-term scalability, strong compliance features, and enterprise-grade payroll and HR tools. It’s a reliable payroll software that ensures that its users spend less time on payroll, and more time on their nonprofit endeavors.

Paycom – Best For Onboarding And Employee Training

Paycom is a cloud-based payroll and HR platform that can help nonprofit organizations improve efficiency, reduce compliance risks, and optimize workforce management. Utilizing a single, user-friendly system, Paycom streamlines payroll, tax filing, time tracking, benefits administration, and HR documentation.

Standout Features

  • Error-free payroll that identifies errors and guides employees to fix them before submission.
  • Thorough background checks that ensure a nonprofit hires reliable workers dedicated to the organization’s mission.
  • A flexible learning management system (LMS) that can create custom training sessions for a variety of situations.

Pricing

Paycom offers a custom pricing model based on organization size and specific service needs.

Disclaimer: The pricing is subject to change.

Why Choose Paycom

Paycom is ideal for nonprofits seeking a solution that enhances accuracy across payroll and HR operations. It’s particularly effective for mission-driven organizations aiming to streamline administrative workflows and maintain transparency with limited resources. Finally, it’s training resources help nonprofits in achieving any unique goals or compliance requirements that they may have.

BambooHR – Best For Employee Experience

BambooHR focuses on employee wellbeing by providing an HR solution that not only simplifies union compliance processes but also tracks and mitigates burnout. It also focuses on simplifying employee management, from hiring and onboarding to payroll and performance tracking, allowing nonprofit teams to focus more on other important matters.

Standout Features

  • Customizable employee database that helps in tracking and serving multiple employee types.
  • People analytics and detailed reporting tools help track team growth and employee well-being.
  • Mobile app for time tracking, approvals, and employee access to payroll documents on the go.

Pricing

BambooHR offers three pricing plans that are designed to accommodate businesses of varying sizes:

  • Core – custom pricing
  • Pro – custom pricing
  • Elite – custom pricing

Disclaimer: The pricing is subject to change.

Why Choose BambooHR

BambooHR is an excellent fit for people-first nonprofit organizations that want to simplify their HR and payroll processes without sacrificing employee experience. Its easy-to-use interface and mobile capabilities make it especially appealing to nonprofits with limited HR staff or distributed teams.

Paylocity – Best For Workforce Engagement

Paylocity HR & Payroll provides a platform that reduces admin burden, navigates compliance and engages employees. It does this by combining automation, real-time reporting, and employee engagement tools in one system, helping nonprofits streamline payroll and improving compliance and workforce retention.

Standout Features

  • Accurate payroll processing with built-in compliance features tailored for nonprofit reporting needs.
  • Provides an employee self-service portal where they can access pay stubs, tax documents, etc.
  • Offers employee recognition tools as well as anonymous employee surveys that help in building a connected nonprofit culture.

Pricing

Paylocity provides customized pricing based on organizational size and selected features.

Disclaimer: The pricing is subject to change.

Why Choose Paylocity

Paylocity is ideal for nonprofits that not only need efficient payroll and HR tools but also value employee engagement and data-driven decision-making. Its blend of automation and community-focused features supports both operational excellence and a people-first culture.

Paycor – Best For Maintaining Compliance

Paycor Software delivers an HR platform that’s built to help nonprofits optimize administrative processes, manage employee lifecycles, and maintain compliance. With features designed for budget-conscious and grant-funded organizations, Paycor empowers nonprofit teams to reduce paperwork, improve reporting accuracy, and create a consistent employee experience.

Standout Features

  • Grants access to tax experts that help nonprofits mitigate risk and ensure compliance.
  • Real-time workforce analytics that help businesses allocate costs properly and avoid overspending.
  • Provides organizations with the ability to build fully branded career sites, allowing nonprofits to convey their message and mission to potential candidates.

Pricing

Paycor offers flexible pricing plans based on organization size and services selected.

Disclaimer: The pricing is subject to change.

Why Choose Paycor

Paycor is well-suited for nonprofits looking to modernize payroll while gaining better visibility into workforce data and compliance. Its all-in-one solution simplifies back-office tasks, making it easier for nonprofits to stay focused on their community impact.

Justworks – Best For Small Nonprofits

Justworks is a Professional Employer Organization (PEO) that simplifies payroll, benefits, compliance, and HR tasks through a unified platform. It’s especially effective for small to midsize nonprofits seeking enterprise-level support without any overhead. Acting as the employer of record, Justworks manages payroll taxes, benefits administration, and labor law compliance—allowing nonprofit teams to stay focused on their mission.

Standout Features

  • Full-service payroll with automated tax filings, direct deposit, and W-2/1099 generation.
  • Access to affordable health insurance, 401(k), and wellness benefits typically reserved for larger organizations.
  • HR support and compliance guidance, including labor law updates and policy templates.

Pricing

Justworks offers 3 pricing plans that are designed to accommodate businesses of various sizes:

  • Payroll - $8/month/employee
  • PEO Basic - $59/month/employee
  • PEO Plus - $109/month/employee

Disclaimer: The pricing is subject to change.

Why Choose Justworks

Justworks is great for smaller nonprofits that need a hands-off approach to payroll, benefits, and HR compliance. With its PEO model and user-friendly interface, it enables growing teams to access enterprise-grade benefits while reducing legal and administrative burden.

Which Payroll Software Should Your Nonprofit Organization Choose?

By now, you’ve had a thorough look at the best payroll software options tailored for nonprofit organizations.

Each platform highlighted here is built to address the unique challenges nonprofits face—whether it's managing grant-funded roles, staying compliant with nonprofit tax requirements, or optimizing limited HR resources. From automation and accurate reporting to employee self-service and integrated benefits, these tools are designed to help you reduce administrative overhead and stay mission-focused.

Still not sure about the software listed here? Try exploring our resource center for more comparisons and in-depth software guides.