This article is part of a larger series on Payroll Services.
As a nonprofit organization, finding a payroll software can sometimes be challenging. While on the hunt for the best fit, it’s important that you look for a provider that has the features you’ll need, like full-service tax filings and quick direct deposits, while remaining within your budget. In this guide, we highlight five different payroll software that can streamline your payroll process so you can focus on what you do best without breaking the bank.
Based on our evaluation, the best payroll software for nonprofits are:
- Gusto: Best overall payroll software for nonprofit organizations, especially those with fewer than 100 employees looking for both payroll and HR support
- QuickBooks Payroll: Best for QuickBooks for accounting users
- Paycor: Best for a robust HR solution
- Patriot Payroll: Best for small nonprofits needing a simple payroll solution
- ADP Run: Best for scalable payroll software to grow with
If you need more information before choosing a provider, check out our easy guide to understanding payroll for nonprofits, where we walk you through everything nonprofit, from unemployment taxes to labor laws.
Best Payroll for Nonprofits Compared
Starter Monthly Pricing
Specific Non Profit Features
Unlimited Pay Runs
Calculates and Files Payroll Taxes
Standard Direct Deposit Timelines
$39 + $6/employee
$45 + $4/employee
$99 per month
$30 + $4/employee
With add-on fees
Gusto: Best Overall Payroll Software for Nonprofits
Gusto is an online payroll software that offers both advanced technology and great add-ons. Given the affordable price and unique Federal Unemployment Tax Act (FUTA) payroll tax exemption feature, Gusto is an ideal payroll solution for nonprofit organizations. On Capterra, Gusto has over 2,000 reviews with a user rating of 4.7 out of 5. Customers love that Gusto is easy to use without sacrificing accuracy. Many reviews highlight the diligent customer service, easy-to-use interface, and robust benefits options.
Gusto’s great customer reviews is just one of the many reasons it ranked first in our guide to the best small business payroll softwares for 2022.
In our evaluation, Gusto earned an overall score of 4.35 out of 5. While Gusto doesn’t currently offer health insurance in all 50 states, like ADP Run, a few of its top-ranking features include pricing, reporting capabilities, and ease of use—which are some of the most important criteria to consider as a nonprofit.
Gusto recently announced its integration with Aplos’ Nonprofit Software. Aplos has everything you need to run your nonprofit, allowing you to streamline all of the most important aspects of your business in one place. Aplos enables you to manage fund accounting and donations and create extensive reporting around financials. Gusto’s new integration takes its software to the next level, allowing your payroll data to seamlessly integrate with your financials.
Software Fees: Gusto currently offers four levels of service. Each provides different features that allow business owners to only pay for what best serves their business’ specific needs. Those four plans are:
- Core ($39 plus $6 per employee, per month): Includes unlimited pay runs, automated payroll taxes, PTO policies, an employee self-service portal, onboarding tools, benefits administration, and new hire reporting
- Complete ($39 plus $12 per employee, per month): Includes all core features plus employee directory, surveys, time tracking, project tracking, and workforce costing
- Concierge ($149 plus $12 per employee, per month): Includes all complete features plus access to Gusto’s HR resource center and contact with certified HR professionals
- Contractor Only ($6 per employee, per month): Unlimited contractor payments, contractor self-service portal, 1099 filings
Additional Costs: Gusto doesn’t charge administration fees for health insurance and workers’ compensation plans, but you will have to pay the applicable premium costs. You may also have to pay participation fees for retirement plans, commuter benefits, college savings, health savings accounts (HSAs), and flexible spending accounts (FSAs)—should you elect to provide those benefits to your employees.
Regardless of which plan you choose, Gusto has a ton of great features that will help you with your nonprofit payroll.
- Multiple funding periods: Gusto’s Core plan allows you to process direct deposit payments in two days. However, if you subscribe to its higher tiers, Complete and Concierge, you will get access to next-day direct deposits. This means you will only have to process payroll one day in advance, a huge benefit for busy nonprofits that need to keep their cash on hand longer. Note: QuickBooks Payroll offers next-day direct deposit in all of its plans and same-day direct deposit in premium ones.
- Employee benefits: Gusto has the ability to broker a ton of benefit plans, including health insurance, 401(k)s, FSAs, commuter benefits, and more. However, unlike QuickBooks Payroll and ADP Run, Gusto does not currently offer health benefits in all 50 states. For the full list of states where Gusto can offer benefits, check out its FAQ.
- Customer support: Gusto’s customer support received a perfect score on Capterra for all of its great features. It has email support, live agents available via phone, and forums/FAQs that you can reference directly from its website. Its phone and email support team can assist you with any and all questions you may have.
- Free payroll setup: Similar to Patriot, Gusto offers a free system setup. Its team will request all relevant information and get everything up and running for you. If you prefer to do it yourself, you can utilize its payroll startup wizard.
- Exemptions: Gusto has a unique feature for nonprofits, allowing you to set up a Federal Unemployment Tax Act (FUTA) payroll tax exemption on your tax setup page. This will automatically prevent FUTA from being deducted—one less thing you’ll need to worry about.
- Third-party software integrations: Gusto’s software integration options include FreshBooks, Xero, QuickBooks, When I Work, Homebase, and Expensify. This flexibility is a huge plus for Gusto. Patriot, for example, only integrates with its own accounting software and QuickBooks.
QuickBooks Payroll: Best for QuickBooks Accounting Users
QuickBooks Payroll offers many of the most important pay processing tools that a nonprofit organization needs at a reasonable price. Given that its payroll function can be directly and easily accessed through the QuickBooks system, it saves QuickBooks users time from having to separately set up a chart of accounts and import pay-related data into its platform. With QuickBooks being a household name for accounting software, this is a huge competitive advantage, especially compared to those with very limited integration capabilities such as Patriot Payroll.
With 4.08 out of 5 in our evaluation, QuickBooks Payroll earned high ratings for pricing, ease of use, and reporting. QuickBooks Payroll received a lot of positive feedback from online reviewers who said that its simple yet efficient tools make running payroll easier for them. However, some users complained that the mobile app can be glitchy and that connecting with the support team via phone can be frustrating and time-consuming.
QuickBooks Payroll Pricing
QuickBooks Payroll offers three different plans that can provide you with a wide range of payroll and HR features to fit the needs of your business. From workers’ compensation administration to a personal HR adviser, QuickBooks Payroll’s tiered plans give nonprofits the ability to choose the plan and pricing that works best for their budget.
- Core ($45 plus $4 per employee, per month): Includes full-service payroll, health benefits, 401(k) plans, next-day direct deposit, and workers’ comp
- Premium ($75 plus $8 per employee, per month): Core plan plus same-day direct deposit, access to its HR support center, and time tracking
- Elite ($125 plus $10 per employee, per month): Premium plan plus tax penalty protection, access to a 24/7 product support expert, and a personal HR adviser
Additional Fees: Payroll tax filing in more than one state costs $12 per month for each additional state (for Core and Premium subscribers only since the Elite plan already covers multistate tax filing). Integrating your payroll with QuickBooks Accounting is also an additional cost, anywhere from $25 to $70 per month. For help deciding which is best for you, check out our QuickBooks Payroll plans comparison.
QuickBooks Payroll Features
- Flexible direct deposits: In addition to check payments, QuickBooks Payroll offers next-day deposits for its Core subscribers and same-day direct deposits for Premium and Elite plan holders. You can approve payroll to pay your employees through same-day direct deposit if you process payroll by 7 a.m. Pacific time, 10 a.m. Eastern time on payday. The quickest direct deposit speed that most of the other providers on our list can offer is next-day funding, so same-day payments are a huge value add for QuickBooks Payroll.
- Customer support: For new users, the provider has a guided setup and expert professionals who can help get QuickBooks Payroll up and running. It also has 24/7 chat and phone support available Monday through Friday during business hours.
- Tax penalty protection: In all of its plan options, QuickBooks will cover their own errors. Included in its Elite plan, QuickBooks will cover the penalty and interest for any payroll tax error for up to $25,000 a year—regardless of who made the error. Experts will also represent you before the IRS and concerned agencies and will help you resolve your issue. Most other providers will only guarantee protection from mistakes they have made, so this is another big differentiator for them.
- Automatic payroll processing: Busy schedule? You’ll never have to worry about processing payroll again. Similar to Gusto, QuickBooks allows you to set up payroll to run automatically for all employees that have standard hours and direct deposit set up.
- Customizable reporting: The ability to customize, run, and export reports is very important for nonprofit organizations to be able to understand their costs. QuickBooks allows you to run multiple worksite reports, payroll deduction, contribution reports, and even vacation accrual reports.
Paycor: Best for a Robust HR Solution
Paycor is a payroll and HR solution that offers a full suite of employee management services in one place. In addition to full-service payroll and tax administration, you can also use Paycor for help with recruiting and onboarding new employees and benefits administration. It’s not the cheapest on our list but definitely still an affordable option. Paycor can be a great fit for nonprofits, as it can fulfill many of the duties of an HR department without the cost of hiring a full-time person.
With a score of 3.9 out of 5 in our evaluation, Paycor got perfect scores for its HR features and popularity. It doesn’t allow unlimited pay runs, however, which hurt it in pricing; it also doesn’t allow you to create new reports in its system.
Paycor has over 2,000 reviews on Capterra and an overall rating of 4.40 out of 5. While there are quite a few negative reviews, many regarding frustrations with its timekeeping module, there are many great reviews about its easy-to-use platform and employee onboarding tools.
Paycor’s pricing is broken down based on the number of employees. Its Small Business pricing is for organizations with 1–39 employees and offers three different plans.
- Basic (starts at $99 per month): Includes payroll and tax filings, PDF-only reporting, access to Paycor mobile, self-service garnishments, and child support
- Essential (starts at $149 per month): Basic plan plus PTO requests and approvals, new hire onboarding, and compliance checklists
- Complete (starts at $199 per month): Essential plan plus integrations with 401(k) and accounting/general ledger providers and access to dedicated HR professionals
Paycor also offers a Mid Market plan for businesses with 40–1,000 employees, which includes the provider’s most advanced HR features. Unlike its Small Business plans, pricing for its Mid Market tier is not readily available online. To receive a quote for this product, clients are required to submit their information and the products that they’re interested in via Paycor’s website.
- Payroll processing: With Paycor’s flexibility, your employees can choose from one of the many payment options it offers (direct deposits, physical paychecks, and pay cards). Like Gusto, Paycor also has the functionality to set up automatic payrolls so you don’t have to worry about it processing payroll each cycle.
- Customer service: Paycor offers one-on-one support from certified HR professionals. It also has live phone support, but it’s available only during business hours.
- HR offerings: Similar to ADP Run, Paycor offers a wide range of HR products that can be a huge asset to growing nonprofits. These include onboarding and training, compliance support, time tracking, and scheduling, and even recruiting and applicant tracking. These high-level HR features are not available with small business software such as Gusto or Patriot.
- Third-party software integrations: Paycor’s current integrations include OnShift, Deputy, Square POS, Indeed, ZipRecruiter, WageWorks, PlanSource, AssureHire, and GoodHire.
- Reporting: When it comes to reports, Paycor has a big selection of standard reports in addition to customizable reports that you can create and download.
Patriot Payroll: Best for Small Nonprofits Needing a Simple Payroll Solution
In our evaluation, Patriot Payroll scored a 3.61 out of 5, gaining points for its affordable software and reporting, and losing points for only offering a four-day direct deposit funding period and lack of HR features. Many other providers on our guide, such as Gusto, offer next-day funding.
Though it may not offer flexible direct deposit speeds, Patriot is the only provider on our list that can suit your needs whether you’re looking for a full-service payroll option or a more affordable DIY version for doing payroll.
With budgeting being such an important aspect of nonprofit financials, Patriot Payroll is a great option for those looking for an affordable solution.
Patriot Payroll Pricing
Patriot is the most affordable provider we have highlighted in this guide. It offers four different pricing options: one self-service and three full-service.
- Basic ($10 plus $4 per employee, per month): Includes access to payroll software, but requires you to handle all payroll taxes yourself
- Full Service ($30 plus $4 per employee, per month): Basic plan plus Patriot will file and pay all federal, state, and local payroll taxes for you
- Full Service with HR Software ($36 plus $6 per employee, per month): Full Service plan plus HR features such as paperless employee files and employee information tracking
- Full Service with HR and Time and Attendance Software ($42 plus $8 per employee, per month): Full Service with HR Software plan plus timekeeping, clock-in, and other time and attendance features
Its plans come with free payroll setup, unlimited payroll runs, accounting software integration, and customizable hours and deductions. Using the full-service plan allows you to file and pay all federal, state, and local taxes, regardless of location, and offers a penalty-free guarantee.
Additional Costs: While Patriot’s DIY approach keeps the price affordable, it also means that many of the features included in the pricing for other providers are at an additional cost for Patriot. These software add-ons include:
- Multistate payroll tax filing: $12 per month, per state
- Time tracking: Starts at $6 per month plus $2 per employee
- Employee Data Management Tools: Starts at $6 per month plus $2 per employee
Patriot also offers 1099-NEC filings for all of your contractors at an additional cost:
# of 1099s
$20 base, plus $2 per additional form
- 60-day free trial: Not sure which plan is best for you? Not to worry! Patriot offers a 60-day free trial for all new customers so that you can try its platform at no cost.
- Free payroll setup: Just like Gusto, Patriot offers a free system setup. Its team will request all relevant information and get everything up and running for you. If you prefer to do it yourself, you can utilize its payroll startup wizard.
- Mobile-friendly: Patriot’s software is 100% mobile-friendly. It allows you to run your payroll directly from your smartphone or tablet, without having to download an app.
- Self-service plan: Coming in as the cheapest option on our list, you can save the most money if you choose to file your payroll taxes on your own using Patriot’s self-service plan. We recommend this plan for organizations with fewer than 10 employees, and those only operating out of one state. Otherwise, a DIY approach can get very complicated when it comes to compliance.
ADP Run: Best for Scalable Payroll Software to Grow With
ADP Run is a cloud-based payroll and HR solution that offers a wide selection of products that cater to businesses of all sizes. Earning a 3.59 out of 5 in our evaluation for its intuitive interface and streamlined features, ADP Run is a great solution for growing nonprofits. From an entry-level plan that’s comparable to the other software on our list to plans that target businesses with up to 1,000 employees, its features are scalable and completely customizable. Its Essential plan includes unlimited payroll runs and no setup fee, although the base fee is more expensive than the other comparable plans on our list. Though more expensive, many of its customer reviews on Capterra highlight its powerful employee management tools.
The other standout factor for ADP Run is the advanced HR features. ADP’s suite includes onboarding support, background checks, training tools, performance management, and many more helpful hiring tools. Even if these are not tools that you need now, it’s important to know that they are available through ADP as your business scales. ADP can give your business what it needs as its demands change, whereas other providers on our list, like Patriot, would require you to transition to a new service as those needs change.
ADP Run Pricing
ADP Run’s packages are organized based on employee count. For businesses with one to 49 employees, there are four available plans that include different levels of payroll and HR support.
- Essential: Basic full-service payroll including tax filings, direct deposits, new hire reporting, and access to ADP’s Mobile Payroll App
- Enhanced: Essential plan plus access to ZipRecruiter, State Unemployment Insurance, and background checks
- Complete: Enhanced plan plus basic HR support
- HR Pro: Complete plan plus enhanced HR support and perks for both you and your employees
Unfortunately, pricing is not available online and its cost structure is not very transparent. Pricing for the Essential, Enhanced, Complete, and HR Pro plans are customized and need to be quoted by an ADP sales representative.
ADP Run also offers four higher-level plans for businesses with over 50 employees. Its Payroll Essentials, HR Plus, Hiring Advantage, and Performance Plus plans all require you to speak with one of its representatives directly to request pricing.
Additional Costs: The preparation, delivery, and filing of W-2s/1099s is an additional cost to the employer. Other additional fees include access to its time and attendance software, workers’ compensation coverage, retirement plans, and health insurance options.
ADP Run Features
- Payroll Software Specific for Nonprofits: ADP’s team of professionals have talked to their nonprofit clients about their challenges and have combined their feedback with ADP’s expertise to provide nonprofit payroll solutions that meet the needs specific to the nonprofit environment. These include simple yet detailed employee hours tracking and up-to-date/accurate records of employees’ certifications and credentials.
- Full-service tax filings: ADP Run automatically calculates, pays, and files all payroll taxes on your behalf (federal, state, and local). In addition, ADP will respond to all tax agency notices you may receive in case there are questions about tax deposits and returns that the provider made for you.
- Hiring solutions: With ADP’s Enhanced plan or higher, you get access to ZipRecruiter, a web-based job board that connects small businesses with qualified job seekers. In addition, you’ll get access to other hiring tools that include background checks and digital onboarding documents. While some of the other providers like Paycor provide tools to help you hire the right employees, access to ZipRecruiter is exclusive to ADP Run.
- HR documents: ADP has a library of key HR documents that you can use for your checklists, best practice guides, and company policies. Aside from HR documents, you also get an employee handbook wizard to help you create a comprehensive handbook based on federal employment laws. However, access to these resources requires a paid subscription to one of ADP’s premium payroll packages.
- Access to certified payroll professionals: With ADP Run, you can get in touch with payroll and HR experts whenever you need them. Paychex is the only other provider on our list that offers 24/7 support. With one of ADP’s premium plans, you can also get legal assistance on employment matters from Upnetic Legal Services.
How We Evaluated Payroll Software for Nonprofits
We compared several of the most popular providers and narrowed it down to the top five, specifically focusing on features that would be most valuable for nonprofit organizations. We looked for payroll providers that offer unlimited pay runs, flexible direct deposit schedules, seamless integrations with third-party software, and the availability of both basic and customized payroll reports.
We evaluated each software based on the following criteria:
35% of Overall Score
Aside from affordable monthly fees (Patriot is the most affordable in our guide), when you’re working within a budget, it’s important to know what additional costs you could incur. For example, Gusto offers unlimited pay runs, while many other providers will charge for every payroll run in addition to your normal pay cycle. Hidden fees and upcharges can take a huge hit on your budget, so we’ve made sure to break down what’s included and what’s extra in pricing. In our scoring, we also took into consideration whether or not the provider offers special pricing or discounts to nonprofits.
25% of Overall Score
We evaluated the providers by many of the features that we think are the most valuable for nonprofits. Unlimited pay runs, quick direct deposits, full-service tax filings and payments (federal, state, and local), and contractor payments are just a few. We also checked whether or not the provider offers a penalty-free guarantee, in the event that it makes a mistake when processing your payroll. Gusto and ADP Run are two of the top-ranking providers here.
20% of Overall Score
10% of Overall Score
The best payroll software for nonprofits includes simple HR tools, such as online onboarding, new hire reporting, and employee benefits. Self-service portals that allow your team to manage their information also hold a huge value. ADP Run and Paycor both earned a perfect score for their robust HR solutions.
5% of Overall Score
We think customer reviews are an important factor, and we want to consider feedback from real customers when grading providers. We checked reviews left on third-party sites like Capterra. Gusto, Paycor, Patriot, and ADP Run all have over 1,000 reviews and an average user rating of 4.0.
5% of Overall Score
Aside from having access to basic payroll summaries, users should be able to customize and create new reports within the system. Reporting is especially important for nonprofits that need an easy way to determine their payroll costs. Gusto, QuickBooks Payroll, and ADP Run all received a perfect score.
Whether you’re looking for a full-service solution or a more DIY approach, our guide can help you determine which software is the right fit for your nonprofit organization. It’s important that you find the best payroll software that has the features you’ll need, like full-service tax filings and quick direct deposits, while remaining within your budget.
Based on our evaluation, we found Gusto to be the best payroll software for nonprofits with an overall score of 4.35 out of 5. It offers affordable plans that start at $39 plus $6 per employee monthly, plus a contractor-only option that costs $6 per person monthly. Gusto is a crowd favorite with its user-friendly time tracking and quick direct deposit options. This makes Gusto the best option for nonprofits that want quality services at a budget-friendly price. Sign up for a free trial.