QuickBooks Payroll vs Paychex (2023): An In-Depth Comparison

With so many great payroll software options available, it can be difficult to choose the right software for your needs and budget. Today, we’ll compare two of the most popular online payroll services, QuickBooks Payroll and Paychex, to help you figure out which one is right for your business.

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What is QuickBooks Payroll?

While Intuit QuickBooks is most famous for its bookkeeping and accounting software, it also offers other solutions, including the cloud-based payroll software we’re reviewing here. Note that the payroll software syncs with QuickBooks Online, but not with QuickBooks Desktop — so if you currently use the desktop version, keep that in mind when considering these two payroll options.

Check out our full QuickBooks Online Payroll review for more details.

What is Paychex?

Paychex is another very popular payroll and HR solutions provider. We’ll focus on Paychex Flex, its cloud-based payroll service, in this review because of its popularity. However, Paychex offers a few other payroll options, such as Paychex PEO. Like many other major payroll providers, Paychex syncs with QuickBooks Online due to pre-built integrations.

Check out our full Paychex review for more details.

QuickBooks Payroll vs Paychex: Comparison Chart

Pricing and details are updated as of 6/22/2023.

QuickBooks Payroll vs Paychex: Pricing

Both QuickBooks Payroll and Paychex offer multiple pricing tiers. QuickBooks is more transparent, disclosing the prices of the three plans and offering a free trial option. Meanwhile, Paychex only reveals the price of one plan (others require a custom quote) and doesn’t offer a free trial option.

quickbooks payroll pricing

• Payroll Core: Cost $45 per month plus $5 per employee per month.
• Payroll Premium: Cost $75 per month plus $8 per employee per month.
• Payroll Elite: Cost $125 per month plus $10 per employee per month.

New QuickBooks customers can choose between a 30-day free trial or a 50% discount (but not both) for three months of service.

See: 5 Best QuickBooks Payroll Alternatives

Paychex Pricing

• Flex Essentials: Cost $39 per month plus $5 per employee per month.
• Flex Select and Pro: Contact for custom quotation.

Paychex does not offer a free trial option, so you will have to decide whether you want to subscribe or not based on the demo only.

See: Gusto vs Paychex: Which Payroll Software Is Better for Your Business?

Feature Comparison: QuickBooks Payroll vs Paychex

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payroll functionality

Both QuickBooks Payroll and Paychex offer all the standard payroll features, although not all features are available for all plans. Both services will automatically calculate pay, deduct payroll taxes, and remit those taxes to you.

Depending on your plan, QuickBooks Payroll offers same-day and next-day payroll. It also provides an option to set up auto payroll, which will run without manual initiation. Meanwhile, Paychex gives employees the option to review their scheduled payments in advance to reduce payroll errors.

WATCH: Best Payroll Software for Accountants in 2023

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time care

Time tracking is one of the most useful additional features for payroll software, as data on hours worked can flow directly into payroll tools. QuickBooks Payroll and Paychex both offer options for time tracking — but not on the base plans.

Time tracking is available on the Premium and Elite QuickBooks plans, while the Paychex Flex Time feature is a paid add-on. Employees can clock in and out time online via mobile app or time kiosk tablet.

See: ADP vs Paychex: 2023 Payroll Software Comparison

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HR features

QuickBooks Payroll and Paychex also include some HR features, although QuickBooks’ capabilities are more limited. QuickBooks offers both 401(k) and health insurance benefits administration, as well as the Workers’ Compensation Administration and an HR help center operated in collaboration with Mineral Inc.

Paychex provides benefits administration for both health insurance and retirement plans, as well as HR services for employee onboarding, HR consulting and the hiring of new employees. It also offers business insurance management for workers’ compensation, general liability, cyber liability, commercial property, and umbrella.

See: FreshBooks vs. QuickBooks Online: Which Accounting Solution Is Best for Your Business?

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ease of use

QuickBooks Payroll’s layout and signature green color palette will be familiar to anyone who’s used its other accounting and bookkeeping software. Even if you haven’t used a QuickBooks product before, the accessible layout is easy to navigate because of the left-hand menu.

Paychex follows a similar design, with a left-hand menu and a dashboard made up of modules. However, due to the large number of features offered, some users report that it has a steep learning curve and that it can sometimes take a while to find the function they’re looking for.

See: Gusto vs QuickBooks Payroll: Which Software is Better for 2023?

customer support

QuickBooks consistently wins praise for its customer support and helpful resources. Chat support is available 24/7 in the US, while phone support is available Monday through Friday from 9am to 8pm EST. The company offers a robust online resource center full of videos, tutorials, and webinars to help users get up to speed.

Paychex offers 24/7 customer support – phone, chat and email options are all available, as well as a knowledge base that you must be registered to access. However, users report that Paychex’s customer support isn’t as available or helpful as it could be, and many reviews complain that it could be improved.

WATCH: Best Payroll Software for Nonprofits in 2023

Pros and Cons of Paychex

pros

• Easy-to-use payroll functionality.
• Includes comprehensive HR features.
• Analysis and reporting for payroll insights.
• Option to add on business insurance.

Shortcoming

• No free trial.
• Pricing is not transparent.
• Additional charges for essential services such as time tracking.
• Customer support may be lacking.

See: Ripple vs Paychex: 2023 Payroll Software Comparison

Pros and Cons of QuickBooks Payroll

pros

• user-friendly interface.
• Robust payroll features.
• QuickBooks Online integration.
• Excellent Customer Service.

Shortcoming

• Higher monthly base price as compared to competitors.
• Have to choose between a free trial and a three-month discount.
• Some key features are limited to the more expensive plans.
• HR features are limited.

See: ADP vs. QuickBooks: 2023 Payroll Software Comparison

Should Your Organization Use QuickBooks Payroll or Paychex?

QuickBooks Payroll and Paychex are both promising payroll options. QuickBooks Payroll combines QuickBooks’ excellent customer support with solid payroll features. However, you’ll need to upgrade to more expensive plans to get the most out of QuickBooks Payroll, which may be too expensive for some small businesses. That being said, it does offer a free trial option, so you can try before you buy.

While Paychex may be lacking on the customer service front, it combines HR tools and support with payroll, which may be attractive to small businesses that don’t want to pay for separate HR software. However, the lack of a free trial or transparent pricing plans may deter some companies.

If none of these options sound like the right fit for your needs, there are plenty of other payroll options out there, including many that integrate seamlessly with QuickBooks’ accounting and bookkeeping software. Check out our list of the best payroll software for 2023 to expand your search now.

review method

To compare QuickBooks Payroll and Paychex, we looked at product documentation, user reviews, videos, product demos, and more. We considered factors such as payroll and HR capabilities, pricing, ease of use and navigation, as well as customer support options.