10 Best Payroll Software for Small Business in 2021

Updated on November 6, 2020
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What Is the Best Payroll Software for Small Business?

  1. Gusto offers the fullest packages for your small business payroll software—at the most reasonable price.
  2. QuickBooks Payroll is the best fit for business owners who use QuickBooks accounting software.
  3. Patriot Payroll is the best low-cost payroll software for small businesses.
  4. Payroll4Free is the best free payroll software.
  5. ADP Payroll is best for businesses that need software they can use any way anywhere.
  6. OnPay Payroll is the best payroll option for businesses with hourly and contract workers.
  7. Paychex Flex is the most scalable payroll product for growing businesses. 
  8. Square Payroll is best for business owners who already use Square for their POS.
  9. Zenefits Payroll best comprehensive option.
  10. Wave Payroll is best for businesses looking to try other software for free.

Making sure you pay your employees in full and on time is a non-negotiable ingredient to a high-functioning team, which makes choosing payroll software for your small business a weighty decision.

Whether you’re looking for a barebones, free payroll software, or you’re willing to pay for full-service payroll software, there are some pretty stellar options out there for you. Here are the four best options on the market right now.

The Best Payroll Software for Small Business

1. Gusto Payroll

Our pick for the best payroll that offers up the fullest package—for the most reasonable price—is Gusto. Gusto is a payroll, benefits, and HR platform that is available to small businesses starting at just $45 a month ($39 as a base price and then an additional $4 per person per month for their least expensive plan.) Gusto also has a new option for contractor-only employers, who simply pay the $6/employee rate and no base price.

All versions of Gusto offer access to full-service payroll. The more you level up, though, the more features you’ll get. Every Gusto plan comes with these features:

  • Full-service payroll software
  • Employee self-service and profiles
  • Health benefits administration
  • Workers’ comp administration
  • Customer support
  • PTO tracking

The Gusto Complete plan is the next level up and has the same $39 base price but is an additional $12 per employee per month. The added features are:

  • Admin permissions
  • Employee offers and onboarding
  • PTO approvals to accompany PTO tracking
  • Employee directory and surveys

The Gusto Concierge plan, the most expensive plan, costs $149 per month and an additional $12 per employee per month with the added features of:

  • Dedicated customer support
  • Certified HR professionals
  • HR resource center

All versions of Gusto payroll software offer a month’s free trial, so you can test them out to see if they’re the right fit. Don’t forget that you can also tack on extra benefits and insurance—like 401(k) retirement plans and health benefits, for instance—to whichever Gusto plan you end up choosing.

To give you an idea of what each of these options entails, let’s run through all three versions of Gusto payroll software:

Get Started With Gusto Payroll

2. QuickBooks Payroll

Another top payroll software option for small businesses is QuickBooks Payroll. If you’re already using QuickBooks accounting software to track your business’s finances, this will be one of the easiest ways to automate your payroll. In fact, if you’re using QuickBooks Online, you’ll be able to turn on this payroll software with the click of a button in your accounting software.

There are three versions of QuickBooks Payroll software that you’ll be able to choose from. The first is QuickBooks Payroll Core, which is the self-service version of QuickBooks Payroll software. This product calculates paychecks, pays your employees, and calculates and files year-end forms. The first three months cost $13.50 per month, along with $4 per employee per month. After those first three months, the base cost increases to $45 per month, but the employee cost remains the same.

If you want more help from your payroll software than the basic version of QuickBooks Payroll can offer you, consider leveling up to the Premium version. With Premium QuickBooks Payroll, you can access all the features that the Self Service version offers, along with these features:

  • Payroll taxes done for you
  • Same-day direct deposit
  • Free W-2s filed and sent for you
  • Assistance setting up payroll
  • User-based permissions
  • Premium time tracking (via mobile app)
  • An HR support center
  • Their no-penalty guarantee for tax filing

For these extra features that Premium QuickBooks Payroll offers, though, you’ll have to pay more—the first three months are $22.50 a month, and subsequent months are $75. Again, each employee costs $8 per month.

Finally there is QuickBooks Payroll Elite—the most comprehensive payroll product QuickBooks offers. This package has everything in the Core and Premium packages, plus:

  • Employee onboarding handled by QuickBooks
  • Time tracking with geofencing
  • Tax penalty-free guarantee
  • Additional customer support for US-based businesses
  • A personal HR advisor

For all of these additional perks, you’ll pay $37.50 for three months. After three months, the rate increases to $125 per month, plus $10 for every employee you add.

Get Started With QuickBooks Payroll

3. Patriot Payroll

Another option on our list of the best payroll software for small businesses is Patriot Software Payroll. Patriot Payroll software comes in two versions, plus you can add two bonus features—time and attendance tracking and HR software—for a monthly fee.

The Basic version of Patriot Payroll software comes with a base cost of $10 a month plus $4 per month per employee. The software has the following payroll capabilities:

  • Payroll setup and support
  • Paycheck or direct deposit payments
  • Flexible payment schedules

The other Patriot option is their Full-Service payroll software. There is a base cost of $30 per month, plus $4 per month per employee. For this extra $20 a month, you’ll gain access to all features of Basic Patriot Payroll, along with:

  • W-2s and W-3s filed for you
  • Federal taxes filed and deposited for you
  • State taxes filed and deposited for you
  • Local taxes filed and deposited for you
Try Patriot Payroll for Free

4. Payroll4Free

If you’re strictly on the hunt for a free payroll software, then your best option is Payroll4Free. If you have fewer than 25 employees on your payroll, then you can access all of the basic features that Payroll4Free offers for no money at all.

These basic features include the following:

  • Payroll processing (for both W-2 employees and 1099 contractors)
  • Direct deposits (to your own bank only)
  • Tax calculations and forms
  • Vacation tracking
  • Outside software integrations
  • HR functions
  • Reporting
  • Live customer support

Beyond those basic features, you can pay Payroll4Free to deposit and file your taxes directly from your payroll software for $12.50 a month. Plus, if you want to transfer direct deposit funds to your employee’s bank accounts—rather than your own—then you’ll have to pay them another $12.50 a month.

Other than those two optional services, Payroll4Free is a completely free option that won’t make you sacrifice too much.

5. ADP Payroll

Advanced Data Processing, also known as ADP, is a huge name in the business software world. Its ADP Run is for small businesses. There are four versions to choose from:  Essential, Enhanced, Complete, and HR Pro plans. No prices are available for the plans online; ADP only provides custom quotes.

Every plan comes with the following features:

  • Payroll via the computer, tablet, mobile app, or phone call
  • Direct Deposit
  • Payroll Delivery
  • Reporting
  • General Ledger Interface
  • New-Hire Reporting
  • W-2s and 1099s
  • Tax Filing
  • ADP Employee Access
  • New Hire Onboarding
  • Employee Discounts

The more expensive plans have human resources management features and tools. If you’re simply looking for a payroll plan, then the basic Essential plan or the popular Enhanced plan will do the trick. This is a great option for business owners on the go because you can use it on your phone in the mobile app, on a tablet, on a computer or even call in to run your payroll.

Get Started With ADP Payroll

6. OnPay Payroll 

If you mainly pay hourly and contract workers, then OnPay may be a great option for you to consider when it comes to a payroll provider. The costs for OnPay are readily available and there’s just one version (no plans to sort through). The cost is $36 per month plus $4 per month per person you pay, whether they’re a contractor, a full-time employee or a part-time employee.

The reason OnPay may be a good fit for your business if you’re paying contractors or part-time employees is that payroll does not run automatically. You have to select the employees you want to pay and then enter their hours or wages before you can run the payroll. You can also run payroll quickly and easily, either from your phone or from a computer, thanks to the fact that it’s a cloud-based service.

Features included with OnPay Payroll services are:

  • Unlimited monthly payroll runs
  • Tax filing and payments
  • W-2 and 1099 forms
  • Pay employees by direct deposit, debit card or printed check
  • The option for multiple pay rates and schedules
  • Unemployment insurance withholding
  • Payroll reports
  • Integrations for accounting and time-tracking
Get Started With OnPay

7. Paychex

Paychex Flex offers several plans for growing businesses. You can start with a lower-tier plan and move to the more expensive and more robust ones as necessary. The simplest plan is the Express Payroll plan, followed by the Paychex Flex Select, Paychex Flex Pro, and Paychex Flex Enterprise plans.

All four of the Paychex plans have these features:

  • Payroll tax administration
  • New-hire reporting
  • Free mobile app
  • 24/7 phone and chat support
  • Employee financial wellness program
  • Direct deposit and paycards
  • Employment and income verification services

When you opt for the next-level plans, you get more features, such as a dedicated payroll specialist to help with tax or payroll questions. You get additional ways to pay your employees, such as via check, as well as analytics and reporting. One drawback about Paychex Flex is that the pricing isn’t readily available on their website, so it can be a little difficult to compare services.

Request a Free Quote From Paychex

8. Square Payroll

You’re probably familiar with Square’s point of sale product, but it also offers a payroll service. If you only pay contractors, Square Payroll has a plan that’s $5 per contractor per month. If you have full-time employees, the plan costs $35 per month plus $5 per person per month.

Some of the features in the full-service payroll product are:

  • Pay employees and contractors
  • Offer health benefits
  • 401k
  • PTO and sick leave tracking
  • Track hours
  • Use the mobile app to pay employees
  • Give employees access
  • Import time cards
  • Tax filing

If you use Square as your point of sale software, then your employees can already easily clock in and out. You can then sync that information with the payroll service so you can easily track hours and know they’re accurate come payday.

Get Started With Square Payroll

9. Zenefits Payroll

Zenefits is an incredibly comprehensive payroll option. Its payroll plan integrates seamlessly with its HR, benefits, and time and scheduling plans. It also has tons of integrations available for business owners to use. There are integrations for everything from productivity, applicant tracking, retirement savings, accounting, travel, employee management and performance management.

Some of the many features of the payroll software are:

  • Automatic prorating for new hires
  • Automated payroll reminders
  • Informational paystubs
  • Pay stub messages
  • Direct deposit
  • Pay for contractors
  • Custom earning codes
  • Multiple pay rates

Three plans Zenefits offers are fairly reasonably priced. The least expensive plan, the Essentials plan, is $10 per month per employee; the Growth plan is $18 per month per employee, and the Zen plan is $27 per month per employee. Higher pricing brings more features.

Get Started With Zenefits Payroll

10. Wave Payroll

Wave offers some pretty good free software for accounting and invoicing, but it also offers payroll software. You do have to pay for it, but if you’re in the market for accounting software too it could be a great time to try both; they sync seamlessly.

The cost of Wave Payroll varies by state because in some states Wave can offer tax services. In states with tax services the cost is $35 per month, plus $6 per active employee or independent contractor you pay. In states where taxes are considered “self-service” the base price is $20.

These features are the same no matter what state you’re in:

  • 100% payroll accuracy
  • Unlimited free direct deposits
  • Self-service check printing
  • Payroll reminders in your email
  • Customer support
  • Employee holds
  • Tax filing where applicable
  • Pay stubs and tax forms for employees

The Bottom Line

With all of these options at your fingertips, how are you to decide on the best payroll software for your business?

Each option has its own pros and cons, but at the end of the day, you’ll need to think primarily about how much help you’ll need with your taxes and payroll setup, and balance that with how much you’re willing to pay every month for your payroll software.

Don’t forget to allow for the additional monthly cost that each of your payrolled employees—and future payrolled employees—will mean for your payroll software. As your small business grows, so will your payroll software expenses.

Maddie Shepherd
Contributing Writer at Fundera

Maddie Shepherd

Maddie Shepherd is a former Fundera senior staff writer and current contributing writer for Fundera. 

Maddie has an extensive knowledge of business credit cards, accounting tools, and merchant services, but specializes in small business financing advice. She has reviewed and analyzed dozens of financial tools and providers, helping business owners make better financial decisions. 

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