Paychex Flex and QuickBooks Payroll are both cloud-based payroll systems designed to help you securely process employee and contractor payments. Both offer multiple pay options, access to health insurance benefits, and an employee self-service tool for viewing pay stubs, paid time-off (PTO) balances, and payroll tax forms.
However, there are some differences in functionalities that may make either QuickBooks Payroll or Paychex a better option for you. In this guide, we’ll take a look at both system’s essential features, but if you’re looking to find the right payroll solution quickly, here are our recommendations:
- Paychex Flex: Best for growing startup companies with plans to scale
- QuickBooks Payroll: Best for small businesses, especially those using or planning to use QuickBooks accounting software
The Why Behind Our Recommendations for Paychex vs QuickBooks Payroll
We recommend Paychex Flex for companies that plan to scale, because they will benefit most from the range of payroll solutions that it offers. You can start out using its more DIY payroll plan (it files payroll taxes and offers unlimited pay runs). Then upgrade to more robust plans as you grow. There’s even a Paychex PEO option you can choose when you’re at the point that your HR manager needs to outsource some duties.
Paychex Flex Pros and Cons
|Payroll tax payments and filings covers federal, state, and local taxes||Its basic small business payroll package is higher than QuickBooks Payroll’s|
|Comprehensive benefits options (health, retirement, HSA, FSA, and financial wellness tools)||Dedicated payroll support is available only in higher tiers|
|Has a suite of HR tools (such as new hire onboarding, background checks, and learning management)||Inconsistent customer support|
|Offers 24/7 live phone support||Occasional software glitches|
We recommend QuickBooks Payroll for small businesses because it’s easy to use, affordable, and is part of a suite of Intuit products that cater to small business needs—and has for decades. The payroll system also integrates seamlessly with QuickBooks accounting software, a favorite of many small business owners, which means all data is synced, so you don’t have to enter it twice.
QuickBooks Payroll Pros and Cons
|Easy of use||Local taxes must be manually entered|
|Seamless integration with QuickBooks accounting||Limited HR features|
|Unlimited pay runs||Employee benefits options aren’t robust|
|Fast direct deposits (next-day and same-day options)||Inconsistent customer support|
If you want to learn about more payroll options before making a decision, check out our guide on best payroll services. If you’ve made a decision but need to end the relationship with your current payroll provider, use our guide on switching payroll solutions to ensure you don’t miss anything.
How We Evaluated Paychex Flex vs QuickBooks Payroll
To differentiate between who QuickBooks Payroll and Paychex Flex are best for, I evaluated the depth of each provider’s HR tools and employee benefits. I also reviewed employee pay and payroll tax processing functionalities as well as the software’s 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.
Paychex vs QuickBooks Payroll Side-by-Side Comparison
Starts at $59 plus $4 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
Payroll Tax Calculations, Payments, and Filings
Federal, state, and local payroll taxes
Federal and state payroll taxes
Employee Benefit Options
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 with an additional cost
Included 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
QuickBooks Time (formerly TSheets) and Intuit products
Dedicated payroll specialist with premium plans
Personal HR adviser with Elite plan
24/7 phone support
24/7 chat support; phone support from Mondays to Fridays (6 a.m. to 6 p.m. Pacific time) and Saturdays (6 a.m. to 3 p.m. Pacific time)
*Note that some of these HR tools are available either as a paid add-on or included in the premium plans.
Common Features Both Paychex and QuickBooks Payroll 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
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 cheaper and comes with unlimited pay runs, automated taxes and forms (federal and state), and next-day direct deposits.
However, if you’re a business owner who needs a flexible and scalable payroll solution then Paychex is the better solution for you. Aside from letting you run payroll online, it has an integrated suite of HR solutions for hiring, onboarding, new hire reporting, and learning management.
Pricing: QuickBooks Payroll Wins
When comparing the cost of both software starter plans, QuickBooks Payroll is more affordable than Paychex. 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 published on its website. To get the pricing details of its premium plans, you have to contact the provider to request a quote.
Paychex’s base tier, called Paychex Go, is also priced a little higher than QuickBooks Payroll’s Core plan. You have to pay $59 plus $4 per employee monthly in order to access Paychex’s online payroll solution and tax filing services (federal, state, and local).
Moreover, off-cycle payroll runs with Paychex Flex plans (other than the base option) cost extra. QuickBooks Payroll helps save you money if you find yourself running payroll off schedule.
- Paychex pricing plans: Three payroll packages; Paychex Go ($59 plus $4 per employee monthly), Paychex Flex Select and Paychex Flex Enterprise (custom priced); employee time and PTO tracking costs extra
- QuickBooks Payroll pricing plans: Core ($45 plus $4 per employee monthly), Premium ($75 plus $8 per employee monthly), and Elite ($125 plus $10 per employee monthly); employee time and PTO tracking are included in the Premium and Elite plans
Payroll Features: Paychex Flex Wins
When it comes to payroll processing, QuickBooks Payroll and Paychex Flex have similar functionalities. Both providers offer employee and contractor payments, year-end W-2 and 1099 reporting, and electronic pay stubs that can be accessed through an online portal. The providers also have a mobile app (for iOS and Android) that allows you to process payroll while on the go.
However, 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 through several ways. Aside from direct deposits, checks, and pay cards, the provider offers a pay-on-demand option. QuickBooks Payroll doesn’t have the said functionality.
When QuickBooks Payroll’s Payroll Features Are Enough
QuickBooks Payroll is an ideal option for employers who often process employee payments—both regular payrolls and off-cycle ones. The provider’s unlimited pay run feature is a cost-saver, especially for business owners who pay their staff on a weekly and bi-weekly basis. Moreover, QuickBooks Payroll’s direct deposit options allow for same-day processing—provided that you subscribe either to its Premium or Elite plan.
Employee Benefits: Paychex Flex Wins
Both Paychex Flex and QuickBooks Payroll enable their clients to access benefit options for their employees. However, Paychex Flex offers a wider selection that includes health insurance, retirement, HSA, FSA, and financial wellness tools. In addition, benefit enrollments are made simpler with Paychex’s self-service tools.
When QuickBooks Payroll’s Employee Benefits Are Best
If you only need access to health insurance and retirement plans, then QuickBooks Payroll may work for you.
HR Features: Paychex Flex Wins
Similar to ADP, Paychex provides a suite of integrated HR solutions that enable you to manage your employees well. Apart from payroll, the provider has time tracking, PTO monitoring, and learning management solutions. Tracking applicants and conducting background screening on qualified candidates are also some of the tools included in its hiring services. Plus, its onboarding software not only lets you automate new hire onboarding, it seamlessly transfers applicable employee data into its payroll platform.
When QuickBooks Payroll’s HR Features Are Enough
If you only require simple HR tools, such as time tracking and PTO monitoring, then QuickBooks Payroll is an ideal option for you. Note, however, that these functionalities are made available through the provider’s QuickBooks Time (formerly TSheets) time tracking solution. Plus, you have to subscribe to either its Premium or Elite plan in order to access the integration.
Paychex Flex vs QuickBooks Payroll: Ease of Use, Customer Support, and Integrations
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 steep 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. to 6 p.m. Pacific time) and Saturdays (6 a.m. to 3 p.m. Pacific time). However, you do get 24/7 phone support if you have an Elite plan.
In terms of assistance from HR professionals, Paychex provides a dedicated payroll expert to clients who subscribe to its premium tiers. Similar to Gusto, Paychex 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 also 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. Plus, like ADP, QuickBooks offers easy access to a personal HR adviser, provided you are an Elite plan member.
Software integration-wise, Paychex can integrate with several platforms like hiring, time and attendance, HR, and accounting systems. Meanwhile, QuickBooks Payroll integrates primarily with Intuit products and QuickBooks Time.
Here are some of the two providers’ integration options:
- Paychex partner systems: BambooHR, Glassdoor, Indeed, SimplyHired, OnShift, Clover, Insight360, QuickBooks Online, Xero, Adagio, Hubworks, Altametrics
- QuickBooks Payroll partner systems: QuickBooks Time, QuickBooks, and Intuit products
Paychex and QuickBooks Payroll: User Reviews
- Paychex: This software earned 4.3 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 internet connection is available. On the other hand, some users complained of having experienced occasional system glitches and inconsistent customer support.
- QuickBooks Payroll: Users who left online reviews rated this software 4 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. There are also mixed reviews about its customer support—many users noted that the support team is helpful, while others said that they received poor service.
With Paychex and QuickBooks Payroll, you get a cloud-based platform that can help you process employee and contractor payments in a secure and timely manner. Both providers offer multiple pay options, payroll tax filings, health insurance plans, and an employee self-service portal. While both may have features that are similar to each other, there are also some functionalities that can make either Paychex or QuickBooks Payroll a better solution for you.
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 a QuickBooks accounting user or just a mom and pop needing to run payroll, QuickBooks Payroll is a better option for you. Its Core starter plan is slightly cheaper than Paychex’s basic payroll package, and you get unlimited pay runs with every plan. Sign up for a free trial.