The Best Payroll Software For Nonprofits in 2023

Need a payroll solution for your nonprofit organization? Check out our list of the top payroll software providers for nonprofits in 2023, with detailed reviews and pricing info.

Nonprofit organizations play a crucial role in society, and must manage their finances and payroll effectively to ensure their operations run smoothly. However, managing payroll can be time-consuming and complex, especially for organizations that rely on volunteers and have limited resources. That is where payroll software comes in handy.

With the right payroll software, nonprofits can automate their payroll processes, save time and money, and focus on their mission. This article will compare the best payroll platforms for nonprofits in 2023 to help you choose the one that fits your organization’s needs and budget.

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Features comparison table for best payroll software for nonprofits

Features Gusto Paychex Rippling Justworks Papaya Global QuickBooks
Unlimited pay runs Yes No Yes Yes Yes Yes
Files payroll taxes Yes Yes Yes Yes Yes Yes
Global payroll No No Yes No Yes No
Benefits administration Yes Yes Yes Yes Yes Yes
Nonprofit software integrations Aplos and Monkey Pod Uncommon Giving Bright Funds No No Kindful, Fundly and DonorPerfect

Top payroll software for nonprofits in 2023

Gusto: Best for integrations with other nonprofit software

Gusto is a cloud-based payroll and human resource management software designed to simplify financial operations like payroll, tax filing, benefits management and compliance. Widely used by businesses and corporations, Gusto also serves nonprofit organizations.

The Gusto logo.
Image: Gusto.

Gusto offers comprehensive payroll solutions that enable nonprofit teams to streamline their financial operations. By automating payroll procedures, Gusto facilitates monitoring employee work hours and payrolls as well as tax-related payments and filings.

The platform integrates with charity donation software like Aplos and Monkey Pod, making it easy for nonprofit owners to flexibly manage their donations. In addition, Gusto’s payroll solution provides managers with convenient access to their team’s financial data, facilitating effective organization and efficiency.


  • Gusto allows employees to track the number of hours they have worked.
  • Employees can contribute to the nonprofit directly from their paychecks.
  • Gusto offers features that assist nonprofits with tax calculations.
  • With Gusto, employers can automate and customize employee pay rates and schedules.
  • Employees can also automate short-term savings on the platform.


  • Offers customizable reporting.
  • Unlimited payroll runs.
  • Lets employees donate from their paycheck using Gusto Giving.


  • Nonprofits are not offered any discount.
  • Insurance is still limited to only 39 U.S. states.


Gusto is priced in three different tiers:

  • Simple plan: This plan starts at $40 per month, plus $6 a month per employee.
  • Plus plan: This starts at $60 per month, plus $9 a month per employee.
  • Premium plan: This pricing plan is available upon request.

Paychex: Best for payroll tax compliance support

The Paychex logo.
Image: Paychex

Paychex is a top payroll software that supports nonprofits. The platform helps organizations calculate work rates, file and manage payroll taxes, and process benefits administration.

The solution caters to small and mid-sized businesses as well as nonprofits. Paychex’s platform simplifies financial activities such as tracking donations, filing taxes and recording expenditures for nonprofits.

In addition, Paychex offers multiple employee payroll processing features that make it easy for organizations to manage different types of payment from their desktops or mobile phones. Depending on the type of payment method your organization offers, Paychex offers payroll options such as direct deposit, paper checks, 24/7 real-time payments and Pay-on-Demand.


  • Paychex has tax compliance support that can assist organizations with federal, state and local laws.
  • The platform also provides employee compensation claims administrations.
  • Paychex offers financial reporting capability for nonprofits.
  • There is time and attendance tracking for managers to generate reports on how employees are doing their jobs.


  • Paychex reports are customizable to suit your business.
  • Offers fast payment.
  • Paychex has a mobile version for easy accessibility on the go.


  • The pricing structure does not suit smaller nonprofits.
  • Pricing for higher plans is not detailed.


Paychex pricing comes in three tiers:

  • Paychex Flex Essentials: Starts at $39 per month, plus $5 per employee.
  • Paychex Flex Select: Pricing is customized based on your needs.
  • Paychex Flex Pro: Customized pricing based on your needs.

Rippling: Best for payroll flexibility

The Rippling logo.
Image: Rippling

Rippling is a U.S. and global HR and payroll platform for both for-profit and nonprofits. Built with a minimalist design, Rippling offers nonprofits a payroll system they can set up and start using without difficulty.

From tax deductions, PTO and 401(k) calculations to HSA or FSA deductions, and filing payroll taxes across all 50 states in the U.S., Rippling takes care of compliance activities for you.

With Rippling, you can utilize the suites of prebuilt reports and customize them for your employee data management. From the payroll dashboards, you can see, analyze and share reports across different departments for seamless decision-making across your organization.


  • Rippling offers over 500 third-party software integrations within their systems.
  • The software offers a unified employee database for managing employee data automatically across all modules, ensuring accuracy.
  • Rippling has features for managing and filing payroll taxes across the U.S.
  • It offers the capability for global payroll, giving organizations more hiring flexibility.
  • Rippling enables organizations to pay employees in their local currency.


  • Rippling offers payroll beyond the walls of the US.
  • The platform comes with a vast app integration.
  • It’s easy to track productivity with employee track codes.


  • Payroll services attract extra fees.
  • There is no free trial.


  • The plan starts at $8 a month per user. You can also get a customized price based on your business needs.

Justworks: Best for compliance

Justworks Logo.
Image: Justworks

Justworks is a cloud-based HR and professional employer organization that provides payroll services to businesses of any size, including nonprofits.

The platform makes it easy for businesses to run payroll through integrated automation features. Business managers can set up their employee profile on the software by selecting the payment method, type of employment and payment mode from the payroll features list.

Aside from payroll, Justworks also helps you to process tax filings for your W-2 and 1099 employees. In addition, you can enjoy more payroll flexibility through their weekly and biweekly payment scheduling or choose to run your off-cycle payments when necessary.


  • Off-cycle pay runs can be done as needed with no extra cost.
  • The platform has tax filing features for W-2 and 1099 workers.
  • Offers payroll services and tax filing in all 50 U.S. states.
  • The platform offers payroll flexibility in a way that allows you to split deposits across multiple accounts.


  • They offer discounts to nonprofits.
  • Justworks offers 24/7 customer support.
  • Offers compliance support.


  • Time-tracking requires an extra fee as a paid add-on.
  • Two-tier-pricing methods might be costly for smaller organizations.


Justworks has two pricing tiers:

  • Basic: This plan starts at $59 a month per employee.
  • Plus: This option starts at $99 a month per employee.

Papaya Global: Best for global payroll management

The Papaya Global logo.
Image: Papaya Global

Papaya Global is a professional employer organization and HR software solution that can offer payroll services to nonprofits on a global scale. Offering payroll services to over 160 countries, Papaya automates accounting activities for businesses such as expense management, payment scheduling and local currency payments.

For nonprofits with a global presence, Papaya makes it possible to pay employees in their local currency without going through the hassle of currency conversion. For better reporting, auditing and analytics, businesses can leverage Papaya’s BI report and analytics to analyze region-specific employment costs and trends.


  • The platform provides assistance with payment processing and benefits administration for employees across over 160 countries.
  • Papaya makes it easy for employees to download payslips in their local languages.
  • The software offers robust reporting, auditing and analytics tools.
  • Employers can leverage Papaya Global to process their employee migration to the U.S.


  • Offers cross-border payment.
  • Offers tax and benefits administration at no extra cost.
  • Businesses are at liberty to tailor their needs to reflect a different pricing.


  • The basic plan covers limited features.
  • Payroll pricing varies per country.
  • There is an onboarding fee.


Although the pricing on Papaya Global can be tailored to suit individual needs, they offer four pricing plans:

  • Payroll: This plan starts from $20 a month per employee.
  • Contractor management: Starts from $25 a month per employee.
  • Payroll intelligence suite: Starts from $250 a month.
  • Global EOR: This plan goes for $770 a month per employee.

QuickBooks: Best for donations and managing grants

Intuit QuickBooks Logo.

QuickBooks is another payroll software offering several essential payroll processing features for nonprofit organizations. The software allows nonprofits to manage expense sorting, categorize expenditures by funds or programs, track and manage donations, and generate custom reports.

Detailed budget-tracking tools are available on QuickBooks that allow nonprofits to track budgets, as well as manage grants and donations. There is also an advanced financial reporting feature for bank reconciliations.

In addition, QuickBooks helps nonprofits to accept donations by debit card, credit card, cash, bank transfer or check. There is also a mobile app for access to the QuickBooks payroll services.


  • QuickBooks allows integration with banks to process donations via debit and credit cards.
  • You can import reports from donation apps like Kindful, Fundly and DonorPerfect to the QuickBooks platform.
  • The software provides compliance assistance to businesses.
  • The platform offers automated reporting capability that helps organizations prepare for annual IRS filing.


  • Offers flexibility in terms of how nonprofits can receive donations.
  • Offers next and same-day debit.
  • It’s easy to sync your nonprofit accounting software.


  • Tax penalty protection only comes with the Elite plan.
  • No 24/7 customer support.


QuickBooks offers three pricing plans for nonprofits.

  • Plus: This starts at $42.50 per month.
  • Advanced: Starts at $100 per month.
  • Enterprise for nonprofits: Starts at $135 per month.

How to choose the right payroll software for nonprofits

Choosing the right payroll software for nonprofits can significantly streamline payroll management and save time and resources. Here are some factors to consider when selecting the right payroll software for your nonprofit organization:


Look for a software solution that includes features that meet your organization’s specific payroll needs. For example, if your nonprofit has hourly employees or different pay rates, make sure the software offers those options. Also, consider whether you need features like direct deposit, automatic tax calculations and the ability to print checks.


Your nonprofit may grow over time, and you don’t want to switch payroll software whenever you add a new employee or expand your organization. Choose a software that can grow with your nonprofit and handle an increasing number of employees and payroll complexities over time.

Support and compliance

Make sure that the payroll software vendor offers reliable support, including technical support, training and assistance with compliance-related questions. It’s also crucial to note that nonprofits are subject to various compliance requirements related to payroll, such as tax-exempt status and IRS Form 990 reporting. Look for payroll software that can handle these compliance requirements and stay up to date with any changes in regulations.


Payroll software should be easy to use, even for people who are not tech-savvy. A user-friendly interface and clear instructions, with published how-to documentation on the software, can help ensure that your staff can easily manage payroll and reduce the likelihood of errors.

Overall, as a nonprofit owner or manager, it is important to be aware of your specific needs and budget and compare them to the features above. For instance, if you are more interested in payroll software that is user-friendly, affordable, supports quick and direct deposit, and offers several integrations, then Gusto, QuickBooks and Paychex can do the job. On the other hand, if your nonprofit has employees on a global scale, Papaya Global and Rippling will be able to serve this purpose.

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