The Best Payroll Services for Small and Large Nonprofits in 2023


Whether you run a global organization or a small neighborhood nonprofit, dealing with payroll can be overwhelming. Yet, we all know it is a necessary part of managing nonprofit employees. Luckily, payroll service providers can take on this task that you may not have the expertise or manpower for. 

We have conducted research into the best nonprofit payroll service providers for 2023. In this article, we share the features and prices of each as well as their capacity to fulfill the needs of either smaller or larger nonprofits. Read on to discover which payroll service company is best for your organization!

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What Do Payroll Service Providers Do?

A nonprofit payroll service provider is a company that offers assistance with the day-to-day task of managing payroll for your nonprofit, or that assumes all aspects of the process. It is true that some nonprofits want more from a provider than just software and automation - they aim to eliminate the need for a full-time human resources department altogether. 

best-payroll-services-for-nonprofits-what-do-payroll-service-providers-doWhat do payroll service providers do? You're about to find out, Trish!

In order to consolidate and simplify payroll management duties, payroll providers offer a variety of services to choose from based on a company’s individual needs and preferences. These services can include:

  • Automatic payroll processing 

  • Tax filing services

  • Tax withholding and wage garnishment

  • Payroll reporting

  • Customer service

  • Integrations with other business processes and software

Pro Tip: Payroll service providers can cover as much or as little of the payroll process your organization needs help with. Before your nonprofit chooses a provider, take some time to determine which features you would actually use. This is important because most payroll companies offer a tiered pricing system, and you do not want to pay for more than you need or even economize to the point that you lack features that would help your company grow! 



Payroll Services for Smaller-Scale Nonprofits

Our first group of top payroll service companies cater to the needs of smaller businesses and nonprofits, and their features and price points reflect this. This is not to say that they cannot handle larger organizations, just that they are known to have the little guys in mind - both because they are economical, and because they emphasize simplicity.


Main Features: 

  • A full-service automatic payroll, with compliance assistance

  • Time and attendance information automatically integrated with payroll

  • Easy employee benefit management

  • Talent management tools like performance reviews and learning modules

  • Hiring and onboarding assistance

  • Insights and reporting 

Why it is Suitable for Smaller Nonprofits:

Gusto’s all-in-one payroll service is an award winner that is targeted toward small businesses and nonprofits. They offer a large menu of features to help organizations without an HR director easily manage all aspects of human resources, even if they are not really familiar with nonprofit payroll laws

Pricing Information: 

Gusto offers a three-tiered pricing platform. 

The Simple version offers automatic payroll and benefits integrations for $40 per month plus $6 per person.

The Plus version offers the benefits of Simple and adds HR tools for $80 per month plus $12 per person.

The Premium version provides scalable payroll and benefits, expert HR, and dedicated support. Contact their customer service team for exclusive pricing options. 

Intuit QuickBooks

Main Features: 

  • Full-service payroll with expert product support and next-day (or same-day) direct deposit

  • Expert payroll review

  • HR support center 

  • Workers’ comp administration

  • Bookkeeping features that integrate with payroll services, including project and inventory tracking

Why it is Suitable for Smaller Nonprofits:

QuickBooks is a great software for smaller nonprofits that are just starting out, as they offer a whole catalog of software to handle your business management needs across the board. You can bundle these tools in any number of ways to give your organization a personalized experience, including their payroll services. If you simply want payroll without the bookkeeping, this is also an option. 

best-payroll-services-for-nonprofits-smaller-scale-nonproiftsMatt is loving all the options he has for a payroll service provider!

Pricing Information: 

Intuit QuickBooks offers a three-tiered pricing platform. 

Payroll Core + QuickBooks Simple Start offers basic payroll services and covers basic accounting needs for $35 per month plus $4 per employee per month.

Payroll Core + QuickBooks Essentials adds extra features including the ability to track billable hours and pay bills. It also offers access to 3 users for $47.50 per month plus $4 per employee per month.

Payroll Premium + QuickBooks Plus gives you all of the aforementioned features as well as HR support and inventory and product tracking. You also get access for 5 users for $77.50 per month plus $8 per employee per month. 

Pro Tip: Springly's accounting software is compatible with QuickBooks, making it an easy option for nonprofits that are looking for a full accounting suite! 


Main Features: 

  • Payroll services including unlimited monthly pay runs

  • Direct deposit and tax filings 

  • Set up and data migration

  • Software integrations

  • A full set of HR tools including automated onboarding flows, e-signing, custom personnel checklists, built-in document templates, and compliance audits 

Why it is Suitable for Smaller Nonprofits:

OnPay payroll services software is designed to manage payroll for small businesses and nonprofits, always keeping growth in mind. Their services are built to expand with your nonprofit, and are simple and intuitive enough that anyone can understand them. 

Pricing Information: 

OnPay prides themselves on simple and straightforward pricing. You receive set-up and the first month for free. Then you pay $40 per month plus $6 per employee. There are no hidden charges or add-on fees, and you get all of their services at one price. 


Main Features: 

  • Payroll that includes off-cycle, vendor, and payments to independent contractors at no extra cost

  • Available time tracking integration

  • Offers benefits like 401(k) and high-quality medical, dental, and vision insurance

  • HR tools for in-person or remote management

  • HR consulting

  • Tax support

Why it is Suitable for Smaller Nonprofits:

This payroll service company is simple to use and personal attention for each of its customers. Their customer service team does not rely on chatbots or phone trees. They are available 24/7 through phone, email, chat, Slack, or SMS. 

Pricing Information: 

JustWorks offers a two-tiered pricing program.

The Basic version offers payroll, benefits, HR tools, and compliance for $59 per month per employee with a drop in price to $49 per month for your 50th employee onward.

The Plus version offers Basic features plus access to medical, dental, and vision insurance for $99 per employee per month with a drop in price to $89 per month for your 50th employee onward.


Main Features: 

  • Payroll services including payment processing

  • Check printing

  • Direct deposit

  • Payroll Reporting

  • Self-service Portal

  • Vacation/Leave tracking

  • Tax compliance

Why it is Suitable for Smaller Nonprofits:

A subsidiary of Paychex, SurePayroll services are designed specifically to cater to the small business or nonprofit. Their promise is that whether a nonprofit has one employee or one hundred employees, they offer the same level of service and industry-leading technology. It also offers a competitively low flat rate. 

Pricing Information: 

SurePayroll offers a flat rate of $29.99 plus $4 per month per employee. Certain features can be added on a la carte such as accounting integrations ($4.99 per month), and multiple state filing ($9.99 per month). 


Payroll Services for Larger-Scale Nonprofits

While it is true that several of the options for small nonprofits can also serve larger corporations, these companies are really known for their powerful, multi-level systems that regularly serve global nonprofit powerhouses!

best-payroll-services-for-nonprofits-larger-scaleSalma is ready to get her nonprofit payroll in order!

Checkwise Payroll

Main Features: 

  • Payroll processing and reports

  • Employee management

  • Secure file transfer

  • HR Services

  • Time and attendance

  • Direct deposit

  • Accounting software integration

Why it is Suitable for Larger Nonprofits:

Checkwise makes a point to offer personalized service to each organization they partner with. They pride themselves on not treating any company "like a number". While they do work with organizations with employees numbering in the hundreds, they assert they work best with medium-sized companies. 

Pricing Information:

Contact Checkwise customer service for pricing options. 


Main Features: 

  • Payroll services

  • Workforce management

  • Human resource tools

  • Talent

  • Benefits

Why it is Suitable for Larger Nonprofits:

Paylocity is a large and flexible all-in-one payroll solution that is affordable for smaller nonprofits, but has software that can support enormous corporations. They are strongly focused on designing technology that improves their patrons’ workplace experience: this can make their software highly attractive to larger corporations that want the most customized experience possible.

Pricing Information:

Paylocity does not offer pricing info on their website. You can submit a request to receive a demo and customized pricing options from a customer service representative. 


Main Features: 

  • Time and attendance

  • Benefits and Insurance

  • HR outsourcing and PEO

  • Compliance services

  • Integrations

  • App marketplace

Why it is Suitable for Larger Nonprofits: ADP Nonprofit is an established and reputable vendor that has over 50 years of experience in the payroll business. Their technology and service has made them a giant in the industry, with around a fifth of all companies in the United States using ADP payroll services. 

Pricing Information:

ADP offers a four-tiered pricing system, but you must sign up with them and log in to obtain a quote. They do offer a three month trial before you buy. Here is what they provide with each payroll package. 

The Essential version offers a basic payroll service.

The Enhanced version expands this basic payroll service to include ZipRecruiter, state unemployment insurance, and background checks.

The Complete version includes all aforementioned services, and adds basic HR services.The HR PRO version offers all of the above, but expands the HR services and adds extra support and perks for both the organization and employees. 


Main Features: 

  • All-in-one payroll and HR services

  • Hiring and Onboarding

  • Time and Attendance

  • Benefits

  • Compliance expertise

  • HR online library

  • 24/7 personal support

Why it is Suitable for Larger Nonprofits:

With an all-in-one platform and flexible features, Paychex systems can easily work with nonprofits of any size. Their extensive and world-class compliance team keeps their clients ahead of the curve, even for large and complex organizations. 

Pricing Information:

Paychex offers a three month trial before buying, and a three-tiered payment platform. 

PayChex Flex Essentials is their budget option, offering basic payroll, tax filing, and support for $39 per month plus $5 per month per employee. 

PayChex Flex Select adds employee training and expert service. Contact their customer service to get a customized price based on your nonprofit needs. 

PayChex Flex Pro offers full service set-up, payroll tax filing, HR tools, and a personal consultation. Contact their customer service to get a customized price based on your nonprofit’s needs.

best-payroll-services-for-nonprofits-larger-scale-nonprofitsSadie is feeling confident with all her newfound knowledge!


Main Features: 

  • Extensive payroll services that are individually tailored to your nonprofit

  • Recruiting and onboarding

  • Career development

  • HR solutions 

  • Real-time audits

  • Governance and security

  • Tax services

  • Analytics

Why it is Suitable for Larger Nonprofits:

Ceridian offers a single solution in global human capital management, with a variety of high-end software and management features rolled into one. Their platform is designed to help any nonprofit, from startup to global giant, manage their entire employee lifecycle. 

Pricing Information:

Ceridian does not disclose its pricing online; contact a representative for a demo and a customized price plan. 


Final Thoughts

Payroll can get complicated. Whether you are just starting a nonprofit or trying to grow an existing one, you have to ensure you cover all of your bases, both legally and in terms of your organization’s individual needs. Questions like "do nonprofits have to report salaries?," "do nonprofits pay payroll taxes?," and "do employees of nonprofits pay taxes?" are all too common. A solid payroll service can help you answer these questions and more, and in that respect save your nonprofit a good deal of time and money while preventing any potential mistakes. 

Examine your budget and take some time to research payroll service vendors. By doing so you can take an enormous amount of pressure off of yourself and your directors and put the focus back where it belongs: on your nonprofit’s mission. 

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💡What is a payroll service provider?

ADP is not a nonprofit, it is a business that offers payroll and other HR solutions to a number of business and nonprofit organizations. Find out more. 

🔑 How much does it cost to use ADP payroll?

ADP does not disclose prices on their website. However, they do offer several pricing options, and a variety of customizable platforms to help find the right fit for your budget. You’ll have to contact one of their customer service representatives to get a hard number. Find out more. 

📝 How do nonprofits set up payroll?

Nonprofit payroll is set up very much the same way for-profit businesses do. Although many nonprofits are 5013c tax exempt, they are still liable for some payroll taxes. The best bet for any startup nonprofit is to contact a payroll service provider to ensure proper compliance to tax law, as well as to simplify and streamline the payroll process itself. Find out more.  

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