Best Payroll Software for Nonprofit Organizations

Don’t waste your time and money with poorly supported, outdated software—our nonprofit payroll system was built for speed, accuracy and ease of use. Download our free payroll system and pay your employees accurately from anywhere in the world using a web-based app. We’ll even share our powerful employee reporting features with you so you can easily manage all information about employee pay rates, time tracking, attendance, job codes (including customized fields), deductions, reporting to funders and more.

Supporting a cause you believe in can be effective and fulfilling, but managing payroll and finances for a small nonprofit organization is different than running a small business.  

– Best for international workforces

Remote screenshot - 10 Best HR Software For Payroll In 2022

Remote’s homepage gives an overview of any updates that require your attention.
Remote is an HR solution for distributed teams that helps companies of all sizes to pay and manage full-time and contract workers around the world. Remote makes it possible for users to take care of international payroll, benefits, taxes, stock options, and compliance in over 50 countries.

Remote gives you the ability to onboard and pay your contractors and employees in a secure, cloud-based platform. You’ll have access to your most important employment documents, data, and HR processes, while Remote takes care of your localized payroll, benefits, compliance, IP protection, and taxes wherever your team works. Remote’s network of HR and legal experts stays on top of the nuances, changes, and complexities of local regulations to ensure full compliance with all relevant legislation at all times.

Remote also partners with powerful HR systems to connect people, payroll, and HR data. Through Remote’s global employee API and native partner integrations, Remote empowers partners to leverage its global infrastructure in their offerings and help more customers scale their global teams faster.

Remote costs from $299/employee/month, based on country selection up to $599. Special pricing is also available for startups and social purpose organizations.

– Best payroll for shift work

Kronos screenshot - 10 Best HR Software For Payroll In 2022

Kronos enables shift workers to request time off, flag additional availability, and plan shift swaps—then connecting the hours-worked data to their automated payroll software.

Kronos is a cloud-based human capital management (HCM) solution for medium-sized and large businesses. The software is easy to set up for both on-premise and SaaS organizations. This software is highly customizable, so you can adapt it to your organization’s needs.

This tool offers a variety of features, but my favorite is its time and attendance application. You can configure the timekeeping solution to match your company’s workforce and goals. The solution’s configuration is simple, yet effective. You can restrict employee access to the online portal based on job responsibility or change/increase benefits on the go, thus simplifying your accounting processes.

I chose Kronos as the best solution for employee shift scheduling because its mobile app is easy to use for normal smartphone users, so your team should be able to punch in their hours without any difficulty.

Kronos offers customized pricing upon request.

Natural HR 
– Best for workforce analytics

Natural HR screenshot - 10 Best HR Software For Payroll In 2022

Natural HR centralizes your employee data and creates in-depth reports for every member of your team.

Natural HR is a human resource system that has a simple interface, so your employees should be able to learn it with minimal training.

One of the things I liked about this software is its ability to collect and interpret workforce data like headcounts by site, gender diversity, and absences by department. Natural HR collects the organization’s data and centralizes it in easy-to-read reports. This can be very helpful for your HR team because it enables them to present actionable insights to management.

I chose Natural HR as the best tool for workforce analytics because it can help the HR department to track absences before payroll and save time when preparing their reports.

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Natural HR offers customized pricing upon request and you can schedule a demo.

Gusto: Best Overall Human Resources Payroll Software

Gusto logo

Overall Score: 4.44 OUT OF 5

  • Full-service payroll with tax payments and filings included in all plans
  • Offers an affordable contractor-only option
  • Employee benefits options include pay advances
  • Unlimited and automatic pay runs

  • Health insurance coverage limited to 39 states
  • Lacks payroll mobile app
  • No dedicated payroll specialist
  • Time tracking and performance reviews included in higher tiers
  • Limited advanced HR tools

Gusto Pricing

  • Core: $39 per month + $6 per employee monthly
  • Complete: $39 per month + $12 per employee monthly
  • Concierge: $149 per month + $12 per employee monthly
  • Contractor-only plan: $6 per person monthly

Gusto is a highly rated and popular small business payroll software with basic HR functions (such as time tracking, hiring and onboarding, new hire reporting, and performance reviews) in its higher-tier plans. It can process both employee and contractor payroll, files the applicable payroll taxes and year-end W-2/1099 reports, and even handles tip credits. Health benefits options are also available, although the coverage is limited to 39 states as of this writing.

Scoring 4.44 out of 5, Gusto earned the highest overall rating in our evaluation due to its intuitive interface, solid payroll tools, reasonably priced plans, and reporting capabilities. Many users also love its user-friendly platform that makes processing employee payments easy for them. However, Gusto lost some points for not providing health insurance in all 50 states and a robust HR solution suite like ADP, Paychex, and Rippling do.

Gusto Features

  • Reasonably priced payroll plans: Gusto’s core product is payroll and it offers its online tools at reasonable rates, with monthly fees that start at $39 plus $6 per employee. This is unlike Rippling and Zenefits, which offer their pay processing solutions as paid add-ons. For those needing to pay contract staff, Gusto has a contractor payroll plan that costs only $6 per contractor monthly. However, it doesn’t compare to Square Payroll’s low-cost, contractor-only option, which is priced at $5 per contractor monthly.
  • Unlimited and automatic payroll runs: Unlike Paychex or ADP, Gusto lets you run payroll as many times as you want and need without having to pay extra. It even has an “AutoPilot” mode that processes your payroll automatically.
  • Multiple payment options: Salaries are remitted to the employees’ accounts either through pay cards or direct deposits. Gusto’s standard direct deposit timeline is two or four days, although it has a next-day option if you subscribe to its higher plans. You can also pay via paper checks, but you have to print your own. If this isn’t an option for you, consider ADP or Paychex as both offer paper checks with signing services.
  • Employee financial assistance: Employees with financial emergencies can get money between paydays through the “Gusto Cashout” option. Available via the free “Gusto Wallet” app, this feature lets your staff withdraw up to 40% or a maximum of $500 ($200 only for the first transaction) of their average paycheck, whichever option is less. Although Gusto considers this a loan, it doesn’t charge interest fees since the requested amount is automatically deducted from the employee’s next paycheck. Aside from Square Payroll and Paychex, which offer early access to earned wages, none of the other providers in this list have a similar feature.
  • Employee benefits: Gusto can manage your benefits plans or integrate your existing broker and eligible health plans into its system for a fee ($6 per eligible employee monthly). It offers a wide range of options that include commuter benefits, HSA/FSA, 529 college savings accounts, and retirement plans. However, Gusto’s health insurance coverage is limited—it isn’t available in Alabama, Alaska, Hawaii, Louisiana, Mississippi, Montana, Nebraska, North Dakota, South Dakota, West Virginia, and Wyoming. For health benefits that cover all 50 states, consider any of the human resource payroll software in this guide except Zenefits (its health plans aren’t available in Hawaii). Note that with Rippling you have to pay extra for its benefits modules.
  • HR tools: Compared to ADP, Rippling, and Paychex, which have feature-rich HR solution suites, Gusto provides only a handful of HR tools that the average small business owner would need. These include online offer letters, state new hire reporting, paid time off (PTO) and time tracking, performance reviews, software provisioning for new hires, surveys to measure employee engagement, and a self-onboarding portal.
  • Access to HR experts: Having access to HR experts who can answer your compliance and HR queries is helpful. With Gusto, you can contact SHRM- and HRCI-certified HR professionals—provided you subscribe to its highest plan.
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QuickBooks Payroll: Best for QuickBooks Users

Quickbooks Online logo that link to

Overall Score: 4.34 OUT OF 5

  • Offers next- and same-day direct deposits
  • Unlimited and automatic payroll
  • Tax accuracy guarantee covers late filing and payment penalties—only if you gave QuickBooks the correct info on time and have sufficient funds on your account to pay taxes
  • Has a separate tax penalty protection program; QuickBooks to cover tax penalties (up to $25,000/year) regardless of who makes the mistake

  • Time tracking and local tax filings included in premium tiers
  • Tax penalty protection available only in highest plan
  • Integrates mostly with QuickBooks products; you need its accounting platform to access third-party software integrations
  • Basic HR features

QuickBooks Payroll Pricing

  • Core: $45 per month + $4 per employee monthly
  • Premium: $75 per month + $8 per employee monthly
  • Elite: $125 per month + $10 per employee monthly

If you use QuickBooks accounting and want a simple payroll solution with basic HR functions, QuickBooks Payroll may be right for you. It allows unlimited pay runs with automated payroll tax payments and filings, including year-end tax reporting. It works with SimplyInsured to provide health benefits and Mineral for HR support. What sets QuickBooks Payroll apart from the other human resources and payroll software in this guide is its fast direct deposits, wherein its standard processing timeline is a next-day option. Other providers may offer a similar service but will require you to either subscribe to its higher tiers (such as Gusto) or use its online payment solution (like Square Payroll with its Square Payments tool).

QuickBooks Payroll earned 4.34 out of 5 in our evaluation with high ratings (4 and above) in reporting, payroll functionalities, pricing, and ease of use. While it also received a score above 4 for HR features, it doesn’t offer advanced HR tools like Zenefits’s compensation planning module, Rippling’s and Paychex’s learning management solutions, or ADP’s job postings to 25,000+ job sites. However, users still appreciate its efficient pay processing tools and fast payment options.

QuickBooks Payroll Features

  • Automated payroll and tax services: QuickBooks Payroll offers full-service payroll with unlimited pay runs, year-end W-2/1099 reporting, and tax filing services. However, if you don’t want to manually input local tax rates into its system and file the applicable local tax forms yourself, then you have to subscribe to its highest plan. Note that the other human resource payroll software we reviewed offer tax filing services that cover all levels (federal, state, and local)—regardless of the plan selected.
  • Fast direct deposits: QuickBooks Payroll processes direct deposits faster than the other providers on our list. It has same-day direct deposits included in its higher tiers and a next-day option as its standard processing timeline. Note that most of the providers in this guide have a standard two-day processing timeline. Square Payroll may also offer next-day direct deposits and even instant payouts, but you need to have an active Square Payments account.
  • Employee benefits: QuickBooks Payroll’s health insurance plans are available in all US states as opposed to those of Gusto and Zenefits, which both have limited coverage (39 and 49 states, respectively). However, it doesn’t have Gusto’s college savings accounts and ADP’s employee discount perks.
  • Tax penalty protection: QuickBooks Payroll offers a tax accuracy guarantee and a tax penalty protection program. The first one covers penalties for late tax payments, provided you gave the accurate information to QuickBooks and have available funds in your account to pay applicable payroll taxes. The second option is only for its Elite plan subscribers, wherein QuickBooks will shoulder tax penalties (up to $25,000/year), regardless of who made the mistake. None of the providers on our list have a tax penalty protection program as robust.
  • HR tools: QuickBooks Payroll’s HR features aren’t as advanced compared to ADP, Paychex, Rippling, and Zenefits. It only offers basic tools that small businesses would need such as employee onboarding, new hire reporting, customizable job descriptions, and time tracking through its QuickBooks Time solution.
  • Access to HR experts: Get answers to your compliance and HR questions through QuickBooks Payroll’s HR advisory services (provided through Mineral). Available for Elite plan subscribers, you can consult with certified HR professionals on critical HR issues either via phone or online. Its services also include helping you create company policies and an employee handbook.
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BambooHR is the best HR software for small businesses.

It’s a complete Human Resource Management System (HRMS) and is trusted by over 20,000 businesses to manage HR tasks. It’s very intuitive, easy to use, and well suited for companies of all sizes.

The cloud-based system focuses on HR tasks like hiring, compensation, onboarding, and company culture.

There’s an applicant tracking system (ATS) that speeds up the hiring process, and performance management features to improve your company culture.

It also includes employee benefits tracking, PTO management, easy employee onboarding, training, and more.

This SaaS tool is big on employee data collection, which makes it easy for business owners to make informed decisions about new hires.

It’s one of the few providers that qualifies as a Human Capital Management (HCM) tool, which helps your employees reach their potential.

Note: We have a worldwide remote team in 27 countries, so we started using BambooHR. They make it simple to manage everything across multiple countries and time zones.

Their Android and iOS mobile app is handy and lets team members manage their information at home or on the go. It also makes it easy to find employee contact information throughout your organization.

BambooHR offers custom pricing based on your business needs. But there are two different plans you’ll choose between.

The Essentials plan has standard HR management features like PTO, benefits administration, document storage, and more.

While, the Advantage plan includes an ATS, onboarding and offboarding features, and advanced reporting functionality.

Since BambooHR doesn’t offer full-service payroll features, we use Gusto and BambooHR together to manage all of our HR and payroll needs.

However, you will find addons for tax filing, time entry and timesheets, overtime pay, and various employee performance review tools and assessments.

BambooHR is designed with small businesses in mind, but it is also used by companies like ZipRecruiter, Grammarly, and Postmates. This software can grow with you as your company grows, and we can vouch for that 100%.

Expert Review: We believe BambooHR is the best HR software for small businesses, hands down. This is why we use it on WPBeginner.


Employees at nonprofit organizations need to understand that they are not the CEOs their organizations rely upon. Payroll software allows these organizations to remain in compliance with local and international laws.

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