Top QuickBooks Payroll Competitors:
The Best QuickBooks Payroll Alternatives for Your Business

Everyone knows Intuit QuickBooks is a popular accounting platform for small businesses. A lesser-known fact is that QuickBooks can help small business owners pay their employees.

Integratable with the core QuickBooks system, QuickBooks Payroll allows you to track employee hours, pay up to 50 workers by check or direct deposit and print annual W-2s. The highest plan option, dubbed QuickBooks Full Service Payroll, adds the help of Intuit’s experts to calculate and file your payroll taxes for you.

In reviews posted on Software Advice, QuickBooks Payroll customers say the system is user-friendly and comes with a ton of online resources to help novice business owners.

That being said, just because QuickBooks Payroll is a popular option doesn’t necessarily mean it’s the right option for you and your business. Whether you found QuickBooks Payroll lacking, or just want to see what else is out there, we’re here to help.

Below you’ll find five cloud-based QuickBooks Payroll alternatives to handle your business’ payroll needs, divided into two categories:

Most Asked-About QuickBooks Payroll Alternatives
Top User-Rated QuickBooks Payroll Alternatives

Let’s see what these comparable solutions have to offer.

Most Asked-About QuickBooks Payroll Alternatives

This first category of alternatives features those products that are searched most often in comparison with QuickBooks Payroll (e.g., QuickBooks vs. Gusto).

Note: You can learn more about our Alternatives methodology here.

RUN Powered by ADP

If you’re looking for payroll expertise, you can’t go wrong with ADP, which is one of the largest providers of payroll software and services in the world. The company’s payroll and HR system, RUN, is designed, like QuickBooks Payroll, with small businesses in mind.

RUN is available in three different packages, which offers users more flexibility than QuickBooks. The basic package, Essential Payroll, includes basic payroll processing, direct deposit, time and attendance and tax filing, while the most advanced package, Complete Payroll + HR, adds functionality for things such as recruiting and background checks. Like QuickBooks, RUN comes with resources such as HR newsletters and helpful documents to stay on top of best practices.

ADP RUN users on Software Advice say the system is easy to set up, support is great and the dedicated mobile app is a handy way to perform necessary tasks on the go. On the other hand, some users say the system has a steep learning curve.

Having trouble telling ADP’s software systems apart? Read our breakdown of ADP’s offerings here.

Paychex Flex

If you’re looking for software with a more robust feature set which still focuses on payroll, Paychex Flex is a great option to consider.

A comprehensive human capital management (HCM) system, Paychex Flex includes modules for payroll, applicant tracking, onboarding, benefits administration, time and attendance and more.

The platform also features a number of self-service options that enable employees to view their pay stubs and shift schedules, request time off, change their health benefits and more. Multi-tiered options are available for customer support, so users can pick a customization that works best for their needs.

Users on Software Advice nearly unanimously praise Paychex’s staff, who they find friendly and helpful. The clean navigation is another highlight. As far as negatives go, some users say integration between the different modules isn’t always seamless and that standard reports can be difficult to find and generate.


Once a dedicated payroll platform called ZenPayroll, Gusto has evolved to become a popular option for small businesses looking to handle needs such as payroll, benefits administration and compliance.

A feature called “Payroll on AutoPilot” allows users to set up their payroll schedule to run automatically without human interaction. Digital paystubs get sent directly to employee inboxes, where workers can see how their income breaks down and even donate a portion of their pay to charity.

Another highlight is Gusto’s ability to pay contractors and handle reimbursements, as well as integrations with a variety of popular accounting systems, including QuickBooks. A compliance checklist is also available to automatically notify you of important tasks.

Gusto’s benefits include its no-frills, easy-to-use interface and speed. Many users say it takes mere seconds to run payroll or pull a needed report. If you’re looking for a system to handle employee time tracking though, you’ll need to look elsewhere.

Top User-Rated QuickBooks Payroll Alternatives

With the popular options covered, this last section of QuickBooks Payroll alternatives details two additional payroll products that have the highest user ratings on Software Advice.

Note: You can learn more about our Alternatives methodology here.

Patriot Payroll

Patriot Payroll is a highly-touted system with a similar setup to QuickBooks Payroll. The platform has a Basic tier that allows users to print checks and W2s and perform direct deposits, and a Full Service tier where Patriot Software experts will handle your federal, state and local taxes for you. There are optional add-ons for time and attendance and personnel tracking as well.

Along with free setup and support, Patriot Payroll offers businesses the ability to compensate employees using a combination of pay methods for no extra charge. A payroll portal allows up to 100 employees to access their paystubs and pay history.

Patriot Payroll users praise the system’s affordability and its ability to take the complexity and confusion out of necessary payroll processes. Few negatives are mentioned, but one consistent critique is that Payroll Software doesn’t offer phone support outside of normal business hours.

APS Payroll

Last but not least is APS Payroll. It offers a single database to manage incomes and deductions and break out wage payments by department, all while automatically checking for errors along the way.

Along with manager and employee self-service capabilities, APS Payroll includes garnishments, direct deposit, paycards and paycheck reconciliation. More than 80 standard reports are available to users along with a customized dashboard for added transparency. APS Payroll customers can also opt in to APS’ other modules to accomplish tasks such as core HR, time and attendance, recruiting and Affordable Care Act (ACA) compliance if they wish to own a more comprehensive workforce management system.

Reviews on Software Advice highlight APS Payroll’s easy implementation process. Users say transitioning to APS Payroll from other services or platforms is quick and painless. The analytics options are another high point. On the flip side, some users say the system can freeze, requiring a quick refresh, and that custom reports can be cumbersome to compile.

Next Steps

All five systems mentioned above are excellent QuickBooks Payroll alternatives. If you’re still not convinced, here are some next steps you can take:

  • Find more alternatives on our payroll software page. We have over 100 systems with payroll functionality that you can sort and filter by reviews, business size, price, industry and more.
  • Talk a payroll software expert. Our software advisors are standing by ready to help! Fill out this short form about your business and payroll needs, and we’ll send you a shortlist of recommended products with price quotes for free.