Payroll Software for Small Nonprofit Organizations

This free payroll software for small nonprofit organizations is a great alternative to more expensive accounting software. Meeting payroll, tax and human resource needs for your small non-profit organization doesn’t have to be difficult or expensive. Our free payroll software for small nonprofit organizations makes running your organization’s finances easy.

Here you will find free payroll or accounting software for small nonprofits. Getting started is easy, thanks to the wizard-style setup, help balloons and friendly language of this free software. Rest assured that your staff payment and time tracking are done accurately. You can be confident that you are reporting correct information to the IRS and other federal agencies.

– Best for small business payroll

Ceridian screenshot - 10 Best HR Software For Payroll In 2022

Ceridian enables you to optimize your team’s schedule with the help of automation.

Ceridian offers both an HCM platform (Dayforce) as well as a payroll platform (Powerpay), making it an all-in-one HR tool or more niche solution, depending on how you buy in. However, thanks to its powerful time management feature paired with comprehensive payroll automation, the solution is ideal for companies that manage part-time or remote employees (think: smaller businesses without a full stack workforce…yet).

The tool offers some cool features, such as retro pay, the ability to calculate the payroll for any specific point during a pay period, or creating manual checks. You can also create different profiles for managers and employees and set up simple process flows.

Even though it’s a complex HR solution, the best thing about this tool is its time-tracking feature. Managers can ensure that each employee punches in correctly, whether they work in-house or remotely, which can be very helpful for distributed teams. You can create automated workflows for your team, and the employees can access timesheets and schedules in real-time.

Thanks to its scheduling automations and time-tracking capabilities, I chose Ceridian as the best tool for small business payroll.

Ceridian offers customized pricing upon request. They offer a free demo.

Zenefits: Best for Highly Regulated Businesses

Zenefits logo

Overall Score: 4.06 OUT OF 5

  • Reasonably priced plans with multiple options
  • Strong compliance tools with HR advisory services
  • Time tracking and employee scheduling included in all plans
  • Unlimited pay runs

  • Payroll and advisory services are paid add-ons
  • Medical, vision, and dental plans not available in Hawaii
  • All plans and add-ons have a minimum five employee requirement

Zenefits Pricing*

  • Essentials: $10 per employee monthly
  • Growth: $18 per employee monthly
  • Zen: $27 per employee monthly

Add-on tools and services*

  • Payroll: $6 per employee monthly
  • Advisory services: $10 per employee monthly
  • Benefits administration using own broker: $5 per employee monthly

*Requires at least five employees.

Annual plans are also available with slightly lower rates.

Zenefits is an HR program to which you can add payroll and HR advisory services—even its most basic plan comes with hiring, onboarding, PTO and time tracking, and document management solutions. It works with insurance brokers to provide health plans in 49 states—Hawaii not included. We found Zenefits is optimal for businesses in highly regulated industries because of its solid tools that not only automate HR and benefits compliance but also monitor your compliance status.

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Earning an overall rating of 4.06 out of 5, Zenefits scored well (4 and up) in nearly all of our criteria given its efficient HR, payroll, and reporting functionalities. Users also like its user-friendly interface and how well its solutions integrate with each other. However, it didn’t rank higher on our list since it doesn’t offer dedicated support, health insurance coverage across all US states, and check printing/signing services, which both ADP and Paychex offer.

Zenefits Features

  • Feature-rich HR platform: Zenefits has a HR solution suite that includes a wide range of essential features. Aside from processing payroll, it can help you onboard new hires, manage compensation plans, monitor performance reviews, and even run employee surveys. However, it lacks the applicant tracking and job posting tools that Rippling, ADP, and Paychex offer.
  • Pay processing: While Zenefits, like Rippling, requires you to purchase its payroll module separately, it comes with all the tools you need to process employee and contractor payments. It also offers payroll tax filing services and year-end W-2/1099 reporting at no extra cost (Paychex and ADP charge additional fees).
  • Time and attendance tools in every plan: Time and attendance tools are included in all Zenefits plans, making it easy for you to capture actual employee time data for pay processing. Note that OnPay doesn’t have this feature, while Gusto and QuickBooks Payroll offer this in their higher tiers. Rippling, ADP, and Paychex also have time tracking functionalities, but as a paid add-on.
  • Employee benefits: Aside from access to employee benefits options (like medical, dental, vision, FSA/HSA, and retirement plans), Zenefits provides online tools to streamline benefits administration. You can use its partner brokers to manage your plans or pay a monthly fee ($5 per employee) to have your own broker administer your benefits.
  • Access to HR experts: Unlike OnPay and Square Payroll, which don’t have HR advisory services, Zenefits has a team of HR and payroll professionals who can provide expert compliance, HR, and employee management advice. However, this service costs extra ($8 per employee monthly).

Square Payroll: Best for Small Retail & Restaurant Businesses Using Square POS

Square Payroll logo

Overall Score: 3.96 OUT OF 5

  • Has a low-cost contractor-only plan
  • Integrates with Square POS
  • Offers fast direct deposits, including an instant payment option
  • Automatic and unlimited payroll

  • Standard direct deposit has a four-day processing timeline
  • A Square Payments account is needed for next-day direct deposits and instant payments
  • Phone support requires a customer code

Square Payroll Pricing

  • Pay employee and contractors: $35 per month + $5 per employee monthly
  • Pay contractors only: $5 per person monthly
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Most people know Square for its POS and payment processing, but it also handles payroll and basic HR functions through its Square Payroll solution. It sets itself apart from most other human resource and payroll software on our list in that it has a low-cost plan for contractors, offers an instant payment option, and connects seamlessly with Square POS.

With an overall score of 3.96 out of 5, Square Payroll didn’t rank high on our list because it lacks expert HR advisers on staff and has limited HR functions. However, its payroll features are strong with tools that include multiple payment options, automatic and unlimited pay runs, year-end W-2/1099 reporting, and automatic payroll tax filings. Users who left reviews on third-party sites like G2 and Capterra also rated it positively for ease of use, affordability, and payroll functionalities.

Square Payroll Features

  • Low-cost contractor-only plan: Priced at only $5 per contractor monthly, Square Payroll has the most budget-friendly contractor-only plan in this guide. Gusto has a similar option but charges a slightly higher monthly fee ($6 per contractor), while the other six human resource payroll software we reviewed don’t have a special contractor plan.
  • Multiple employee payment options: Employee salary payouts can be made through direct deposits, paychecks, and via its “Cash App.” While the standard direct deposit processing timeline is four days, this can be shortened to a next-day option and even instant payments if you have a Square Payments account. Plus, like Gusto and Paychex, it has an on-demand pay feature that enables employees to withdraw a portion of their earned wages in case of financial emergencies.
  • Payroll tax filing and reporting: Square Payroll offers automatic payroll tax filings for all levels (federal, state, and local) at no extra cost. This is unlike Paychex, which charges fees for some of its tax services, and QuickBooks Payroll, which requires you to upgrade to its highest tier if you want local tax filings. Square Payroll will also prepare and file W-2 and 1099 tax forms at year-end—a service that costs extra with ADP.
  • Square POS integration: Given the seamless connection between Square Payroll and Square POS, you can easily import tips, commissions, and even employee time data for pay processing.
  • Employee benefits: Some of Square Payroll’s employee benefits options include health insurance, retirement plans, and workers’ compensation. If you prefer a wider selection, consider Gusto (offerings include a college savings plan), Paychex (has financial wellness tools), and ADP (provides employee discounts).
  • HR tools: Square Payroll’s HR functionalities are limited to new hire reporting, employee onboarding, and PTO tracking. It can capture employee clock-ins/outs but through the Square POS and its Square Team app. If you’re looking for advanced HR features, Rippling, ADP, Paychex, and Zenefits are great options.



Gusto is the best payroll software in terms of features and ease of use. They offer a ton of functionality and flexibility, so you can create the ideal payroll and HR setup for your small business.

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It’s used by over 100,000 small businesses, just like you.

The cloud-based payroll system is simple to set up, plus it gives your workers a dashboard to manage their employee information.

You’ll find standard payroll management features like automatic deductions and filings, direct deposits, and W-2s and 1099s.

It will automatically calculate and file local, state, and federal taxes. There are also plenty of integrations with popular accounting software like Quickbooks, Clover, Xero, and more.

Note: We use Gusto at WPBeginner to manage payroll for remote team members across different states. We started using Gusto back when it was called ZenPayroll and have been loving it since then.

When we were smaller, we used their HR features, but we’ve outgrown it since our team is now worldwide, and Gusto doesn’t support non-US team members.

However, their platform is packed with enough HR functionality to be an all-in-one tool for most US based small businesses.

For example, you can set up employee health insurance enrollment, 401k, workers comp, commuter benefits, and employee savings programs.

Gusto has a range of employee onboarding features like custom offer letters, document signing and storage, onboarding checklists, even software account creation and management.

There are also time tracking tools, compliance paperwork filing, anonymous surveys, and virtual org charts for users on the higher plans.

Best of all, Gusto offers month to month pricing. So, there’s less risk when moving or starting your new payroll system.

The plans start at $19 per month for small teams of 1 to 2 people. Most small business owners will find the Core plan the most valuable, it starts at $39 per month. Higher level plans give you more features like time tracking.

Expert Review: We believe Gusto is the best payroll software for small businesses. They offer a hassle-free experience, and the best part is that they don’t nickel and dime you like payroll services from your bank or some other larger well-known industry players.


Small nonprofit organizations that need to track their payroll, accounts payable and receivable, and general ledger often find it difficult and expensive to purchase a robust accounting solution. Enhanced Payroll and Accounting Software for Small Nonprofit Organizations is designed specifically for these organizations. This software enables you to enter employee time cards, process time sheets and generate payroll reports. It tracks hours worked by employees. It helps in the payment of invoices received from customers, vendors, subcontractors and others. And it provides the small organization with features not found in other accounting software such as balance forward accounting methods and the ability to produce financial reports within your Microsoft® Excel® spreadsheets.

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