Skip to content
Jobber Academy
Managing Your Business

Best Payroll for Small Business: Top 8 Software Solutions

February 7, 2024 7 min. read
Read More Start Trial

Managing employees is already a lot of work—and the process of paying your team can be an added headache.

Make payroll a quick and repeatable process by choosing a strong payroll system that’s built for small businesses like yours.

There are lots to choose from, so we’ll help you narrow it down. Here are the 8 best payroll software solutions for small businesses that are fast, easy to learn, and affordable.

1. Gusto

Gusto is the best payroll system for small businesses that want to keep payroll simple. It was voted the best overall payroll software by Nerdwallet, and was at the top of several year-end lists for payroll software in 2023.

Payroll run in Gusto

Running payroll in Gusto is incredibly easy—the software breaks it down into a four-step process. It’s also easy to make updates to employee pay details, like hourly rate, at every step.

Gusto doesn’t hide its best features behind big price tags. Even on its most basic plan, Gusto lets you perform unlimited payroll runs, calculate and file payroll taxes automatically, and manage employee benefits.

It also offers a cheaper “Contractor Only” plan if you work with independent contractors (1099 employees) or haven’t hired salaried workers yet.

• Simple employee onboarding experience
• Clear and concise tax information
• Easy employee self service portal
• Offline clock-in and clock-out timer
• Unlimited chat, email, and phone support
• No dedicated mobile app

Save even more time by prepping your payroll in the same place you schedule and manage your team.

Jobber handles your time tracking, including having your team members clock in and out through the Jobber mobile app.

Gusto's integration in Jobber

Once approved, your timesheets and reimbursable expenses sync to Gusto where your payroll is processed.

2. Patriot Software

Patriot stands out as a payroll solution with a great setup process and lots of flexibility. If you’re running payroll for the first time, Patriot could be a good place to start.

Entering hours and money into Patriot Software for payroll

During the setup process, Patriot teaches you the fundamentals of payroll processing, along with links to helpful resources and state-specific compliance information.

Once you’re set up, Patriot lets you process salaried employees, hourly employees, and contractors in the same pay run. Many competitors force you to process contractor pay separately.

Patriot also gives you flexible options for the types of pay your employees can receive and the hours they can work (like holidays, double time, etc).

• Comprehensive setup process
• Easy employee portal
• Make contractor payments
• No dedicated mobile app
• Can’t export reports as PDF or Excel files
• Setup process is too slow for experienced payroll software users

3. OnPay

OnPay offers payroll processing and human resource management on a sleek and straightforward platform.

Payroll run in OnPay payroll software

Like most payroll software, OnPay automatically calculates payroll taxes, lets you customize how you run payroll, and gives your employees access to pay records.

Similar to Patriot Payroll, OnPay works hard to educate business owners who are new to payroll processing and employee management.

The platform offers regular updates and resources that keep you updated with payroll tax laws and regulations. You can also create employee handbooks to support your onboarding process.

• Transparent pricing with a simple pricing model
• First month and setup are free
• Phone, email, and live chat support
• No fully automated payroll approval
• Can’t process bonuses or commissions
• Can’t manage paid time off

4. RUN Powered by ADP

RUN Powered by ADP is a good payroll solution for teams that want to bundle it with their accounting software.

RUN Powered by ADP payroll software

With accounting tools on the same platform, RUN keeps your financial and employee management systems in one place.

While automating your payroll tax filings and making accurate calculations, RUN also offers:

  • Direct deposit for employees
  • Garnishment payment services
  • Detailed, customizable payroll reports

RUN connects with tons of other software programs, including QuickBooks Online, ZipRecruiter, and 7Shifts. Employees can also track time from the RUN mobile app.

• First three months are free
• Payroll packages are easy to create
• Real-time reminders for pay periods
• Workers’ compensation insurance
• Charges setup fees (unless you go with a contract)
• Lack of pricing transparency
• Need to purchase a separate plan to pay 1099 contractors

5. QuickBooks Payroll

QuickBooks Payroll is an additional tool that’s bundled with QuickBooks Online, a top accounting app for small businesses. This payroll service is great for teams that are already comfortable with QuickBooks Online.

Payroll report in QuickBooks Payroll

You can complete every payroll processing task you need to in QuickBooks Payroll, including automated tax calculations, giving employees access to pay records, and reporting.

If you’re not already using QuickBooks Online, consider a simpler alternative like Gusto.

• More advanced payroll tax calculations than other apps
• Includes job costing feature
• Unlimited payroll runs
• No self-serve payroll onboarding for employees
• Must pay additional filing fees for employees in other states
• 24/7 support only available on their Elite plan

Pro Tip: Using QuickBooks Online already? Connect it with Jobber to keep your payment and client data accurate.

6. Paychex

Paychex is another beginner-friendly payroll solution that stands out with great customer support.

Running payroll in Paychex software

Because it’s also HR software, Paychex lets you create very detailed profiles for your employees.

In these profiles, you can store as much information as you need using an unlimited number of custom fields—which very few payroll services offer.

Paychex packs a lot of information on-screen, which can look overwhelming compared to software programs like Gusto. But Paychex users do get a dedicated payroll specialist as a go-to contact for questions or issues.

• 24/7 live phone support
• Process bonuses and commissions
• Manages paid time off
• Access to expert tax services
• More expensive than most payroll software
• Interface can be cluttered and overwhelming

7. Payroll4Free

Payroll4Free is a completely free payroll software for teams of 10 or less.

Running payroll in Payroll4Free

It’s a straightforward program where you can complete basic, essential payroll functions, including calculating taxes and paying via direct deposit.

While Payroll4Free offers unlimited payroll runs, customization for payroll settings and reports is limited compared to most paid alternatives.

• Offers optional full-service tax filing support
• Very helpful customer support reps
• Pay employees and contractors
• Only compatible with Windows
• Ads within the software
• Doesn’t integrate with other apps

READ MORE: 30 small business tax deductions to save money when filing

8. Justworks

Justworks is comprehensive HR and payroll software that can act as your full service payroll and HR team. On top of payroll, it handles insurance, employee training, and tax compliance.

Justworks payroll report

Justworks is great for growing teams that have complex payroll and HR needs. You can create employee handbooks, report on new hire performance, create and manage offer letters, and find templates for workplace policies.

You can also pay employees in different countries in their currencies. If you don’t mind paying more for all these features, Justworks is a solid option.

• Includes time tracking and expense management feature
• Choose from multiple salary structures
• Employee deposits take long to process
• Slow mobile app
• Limited third-party integrations

How to choose the best payroll software

You could run your payroll using any payroll service we listed above. But to choose the best one, consider these factors:

  • Features. What payroll functions do you want, aside from the basics? Do you need a wider set of employee management and HR tools? Or just the basics, like tax filing and pay reports?
  • Team size. Are you paying two employees or twenty? Keep in mind that some apps only accommodate a certain number of users before you have to pay for more or choose a higher-tier plan.
  • Cost. What are you willing to pay for? Will more advanced pay record reporting, salary structure options, and automation be worth a higher subscription price? Or are you happy with basic payroll service at a lower cost (or no cost)?

There isn’t one payroll app that fits all small businesses—so come back to this guide when you need help choosing one that fits the way you work.

Join over 200k service professionals that trust Jobber

Get Started