This article is part of a larger series on Payroll Services.
Paychex Flex and QuickBooks Payroll are cloud-based payroll systems designed to help you process employee and contractor payments. QuickBooks Payroll allows unlimited pay runs and integrates with Intuit products like QuickBooks (a popular small business accounting software), while Paychex Flex has scalable payroll solutions (from a one-person plan option to enterprise or PEO), more robust benefits options, and a higher level of HR support that’s great for businesses planning to grow significantly.
In this guide, we’ll take a look at both systems’ essential features, but if you’re looking to find the right payroll solution for your needs quickly, here are our recommendations:
- Paychex Flex: Best for growing startups with plans to scale
- QuickBooks Payroll: Best for small businesses, especially those using QuickBooks accounting software
When neither Paychex Flex nor QuickBooks Payroll works for you, we found that Rippling is the best alternative, as it lets you mix and match HR, IT, and payroll modules.
- Rippling: Best payroll software for companies employing remote or global workers or wanting a modular solution
QuickBooks Payroll vs Paychex Side-by-Side Comparison
Starts at $39 plus $5 per employee
$45 to $125
plus $4 to $10 per employee
Paper check, pay card, pay-on-demand, and direct deposit
Paper check, pay card, and direct deposit
Automated Payroll Tax Calculations, Payments, and Filings
Federal, state, and local
Federal and state
Health insurance, retirement, flexible spending account (FSA), health savings account (HSA), and financial wellness tools
Health insurance and retirement
Time and PTO Tracking
Available in all tiers but at an additional cost
Only in premium plans
Other HR Tools*
Background checks, employee screening, recruiting, new hire onboarding, and learning management
“HR support center” (includes access to onboarding tools and compliance experts)
Banks, accounting tools, and HR-related software like Xero, Glassdoor, SimplyHired, and BambooHR
Payroll specialist with premium plans
Personal HR advisor with Elite plan
24/7 phone support
24/7 chat support;
phone support from Mondays to Fridays (6 a.m.–6 p.m. Pacific time) and Saturdays
(6 a.m.–3 p.m. Pacific time)
*Note that some of these HR tools are available either as a paid add-on or included in premium plans.
Takeaway: If you’re a small company looking for an affordable payroll software, consider QuickBooks Payroll. Compared to Paychex, its starter plan (which costs $45 plus $4 per employee monthly) is more cost-effective because it comes with unlimited pay runs, automated taxes and forms (federal and state), and next-day direct deposits.
Paychex becomes the better solution if you need a flexible and scalable payroll solution. Aside from letting you run payroll online, it has an integrated suite of HR solutions for hiring, onboarding, new hire reporting, and learning management. You can sign up for its solo (for one-person businesses), small business, enterprise, or professional employer organization (PEO) package.
Both QuickBooks Payroll and Paychex offer:
- Employee self-service and mobile apps (iOS and Android)
- Pay processing for employees and contractors
- Year-end tax reporting (such as W-2s and 1099s)
- Health insurance plans available in 50 US states
- Standard and customizable reporting
Most Affordable: QuickBooks Payroll
$45 to $125
plus $4 to $10 per employee
Starts at $39 plus $5 per employee
Tax Filing and Payments
Federal and state are calculated, filed, and paid for; no added fees for end-of-year filings
Federal and state are calculated, filed, and paid for; charges for end-of-year filings
Yes, through third-party
Added fees to manage in-house benefits
24/7 chat support; phone support available Mondays through Fridays (6 a.m. to 6 p.m.) Saturdays (6 a.m. to 3 p.m.)
24/7 support via phone, chat, email
Here, we compare the cost of both starter plans. While QuickBooks Payroll is more expensive upfront than Paychex, it’s actually more affordable in the long run with unlimited payroll runs and no setup fees.
With its Core plan, which is priced at $45 plus $4 per employee monthly, you get full service payroll with unlimited pay runs, year-end filings of W-2s and 1099s, and automated payroll payments, taxes, and forms (federal and state). Plus, you are granted access to health insurance and retirement plans, including expert payroll support and an employee self-service portal.
In addition, QuickBooks Payroll’s pricing is transparent across the board—enabling you to easily select the plan that fits your budget and business’s requirements. This is unlike Paychex, wherein only the cost of its starter package is on its website. To get the pricing details of its premium plans, you have to contact the provider to request a quote.
Moreover, with Paychex Flex, off-cycle payroll runs (other than the base option) cost extra. QuickBooks Payroll helps save you money if you find yourself running payroll off schedule.
Best in Payroll Features: Paychex Flex
What sets Paychex Flex apart from QuickBooks Payroll is its payroll tax filing services. Paychex Flex automates federal, state, and local tax calculations and stays abreast of any rate changes—while QuickBooks Payroll requires that you set up all local taxes and rates in the system yourself.
Paychex Flex also lets you pay employees in several ways and select a pay period (weekly, biweekly, and monthly) or create a customized payroll schedule. Aside from direct deposits, checks, and pay cards, it offers a pay-on-demand option. QuickBooks Payroll doesn’t have that functionality.
However, QuickBooks Payroll is an ideal option for employers who process employee payments often—both regular and off-cycle payrolls. The provider’s unlimited pay run feature is a cost-saver, especially for business owners that pay their staff on a weekly and biweekly basis. Moreover, QuickBooks Payroll’s direct deposit options allow for same-day processing—provided that you subscribe either to its Premium or Elite plan.
When it comes to payroll processing, QuickBooks Payroll and Paychex Flex have similar functionalities. Both offer employee and contractor payments, year-end W-2 and 1099 reporting, and electronic pay stubs, which can be accessed through an online portal. They also have a mobile app (for iOS and Android), allowing you to process payroll while on the go.
Best for Employee Benefits: Paychex Flex
Both Paychex Flex and QuickBooks Payroll enable their clients to access benefit options for their employees. However, Paychex Flex offers a wider selection, which includes health insurance, retirement, HSA, FSA, and financial wellness tools. In addition, benefit enrollments are made simpler with Paychex’s self-service tools.
If you only need access to health insurance and retirement plans, then QuickBooks Payroll may work for you.
Best in HR Features: Paychex Flex
Paychex provides a suite of integrated HR solutions that enable you to manage your employees well. Apart from payroll, it has time tracking, PTO monitoring, applicant tracking, background screening, and learning management solutions. Plus, its onboarding feature lets you automate new hire onboarding and seamlessly transfers applicable employee data to payroll.
However, if you only require simple HR tools, such as time tracking and PTO monitoring, then QuickBooks Payroll is a good option. Note, however, that these functionalities are available through QuickBooks Time—and to access this integration, you have to subscribe to QuickBooks Payroll’s Premium or Elite plan.
Best in Ease of Use & Customer Support: Tied
Paychex Flex and QuickBooks Payroll both have user-friendly platforms, but the latter is more intuitive and easier to learn. While Paychex Flex is fairly easy to use for employees, it has a slightly steeper learning curve for system administrators.
For customer service, Paychex offers 24/7 phone support, while QuickBooks Payroll has round-the-clock chat support. QuickBooks Payroll also offers live phone support, but the service is available only from Mondays to Fridays (6 a.m.–6 p.m. Pacific time) and Saturdays (6 a.m.–3 p.m. Pacific time). However, you do get 24/7 phone support on the Elite plan.
In terms of assistance from HR professionals, Paychex provides a dedicated payroll expert to clients who subscribe to its premium tiers. It has a team of HR experts whom you can contact to ask questions—but you need to pay extra to get this service.
QuickBooks Payroll offers a similar HR advisory service. Given its partnership with Mammoth, Premium and Elite subscribers can access its “HR support center.” This feature lets you get expert answers for HR and compliance-related queries. It also comes with customizable job descriptions, onboarding checklists, and employee handbooks. QuickBooks also offers access to a personal HR adviser, provided you are on the Elite plan.
Best for Third-party Integration: Paychex Flex
Paychex can integrate with several platforms like hiring, time and attendance, HR, and accounting systems (such as BambooHR, Glassdoor, Indeed, SimplyHired, OnShift, Clover, Insight360, QuickBooks Online, Xero, Adagio, Hubworks, and Altametrics). Meanwhile, QuickBooks Payroll integrates primarily with Intuit products.
Paychex vs QuickBooks Payroll User Reviews
- Paychex: This software earned 4.2 out of 5 stars and 4.1 out of 5 stars from G2 and Capterra, respectively. Reviewers like that it is simple to set up and easy to use, especially for employees. They also appreciate that it is cloud-based, allowing them to check their pay stubs and time transactions from anywhere—provided an internet connection is available. On the other hand, some users complained of having experienced occasional system glitches and inconsistent customer support.
- QuickBooks Payroll: It has 3.6 out of 5 stars on G2 and 4.5 out of 5 stars on Capterra. Most clients like its user-friendly interface, adding that it helps take the stress out of processing payroll. However, there are mixed reviews about its customer support—many noted that the support team is helpful, while others said they received poor service.
How We Evaluated Paychex Flex vs QuickBooks Payroll
To differentiate between when QuickBooks Payroll or Paychex Flex is best, I evaluated the depth of each provider’s HR tools and employee benefits. I also reviewed employee pay and payroll tax processing functionalities, pricing, and ease of use. Customer support was also a major consideration since that plays an important part in setting up a new payroll system.
If you want robust payroll tax administration that includes automated calculations, payments, and filing of federal, state, and local taxes—then consider Paychex. It also provides you with a variety of benefits options (like FSA, HSA, health insurance and retirement plans, and financial wellness programs) that you can offer to employees.
However, if you are—or plan to be—a QuickBooks accounting user or a mom-and-pop needing to run payroll, QuickBooks Payroll is the better option. Its Core starter plan is slightly cheaper than Paychex’s basic payroll package, and you get unlimited pay runs. Sign up for its free trial.