QuickBooks Payroll vs Paychex Flex

Whether you’re hiring your first employee and getting payroll set up for the first time, or you need a payroll solution to keep up with your business’ growing needs, choosing the right provider for you is of the utmost importance.


Both QuickBooks and Paychex are two of the most popular payroll software options. So here are all the details about features, pricing, and functionalities for each, so you can decide which is a better fit for your business.

Whether you’re hiring your first employee and getting payroll set up for the first time, or you need a payroll solution to keep up with your business’ growing needs, choosing the right provider for you is of the utmost importance.

Jump to compare QuickBooks and Paychex by:

Ratings and Reviews | Pricing and Features | Support

Compare ratings and reviews

Users of QuickBooks Payroll and Paychex as well as experts in the industry have shared their opinions about both providers. Check out what they have to say about each company in these reviews. But keep in mind, neither Paychex or QuickBooks take the top spot when it comes to customer satisfaction.


See who's the top-rated provider
Customer ratings Expert reviews

QuickBooks Payroll

Paychex Flex

Ease of Setup

76%
84%

Ease of Admin

90%
87%

Quality of Support

80%
86%

Performance

89%
88%

Reliability

89%
89%

Customization

Not available
77%

Reporting

Not available
86%

Based on G2Crowd ratings

QuickBooks Payroll

Ease of Setup

76%

Ease of Admin

90%

Quality of Support

80%

Performance

89%

Reliability

89%

Customization

Not available

Reporting

Not available

Paychex Flex

Ease of Setup

84%

Ease of Admin

87%

Quality of Support

86%

Performance

88%

Reliability

89%

Customization

77%

Reporting

86%

Compare features and pricing

Depending on the provider you choose, certain features and functionality may come at an additional cost or may not be available at all. Here’s a breakdown of all the features included in QuickBooks Payroll and Paychex, and which ones you may have to pay a little extra for.

QuickBooks Payroll Paychex Flex
Pricing
Base price Starts at $45 per month Tiered pricing No published price. Negotiate with sales. Price is per pay run, not monthly.
Per worker cost Starts at $4 per person Tiered pricing No published price. Negotiate with sales. Price is per pay run, not monthly.
Full-service payroll
Automated federal, state, and local tax filings and payments Included Included
Unlimited pay runs Included Additional fees
Multi-state payroll Included Additional fees
Edit or cancel a pay run Additional fees Additional fees
Multiple pay rates and schedules Included Included
Garnishments Included Included
Accounting and time tracking integrations Included Time tracking integration: Included

Accounting integration: Additional fees for some providers
New hire reporting Included Included
Year-end filings, W-2s, and 1099s Additional fees Additional fees
Onboarding and Employee Self-Service
Employee self-onboarding Included Additional fees
Employee self-service portal Included Included
Document e-sign for I-9s and W-4s Additional fees Additional fees
Send and sign offer letters electronically Not available Not available
Employee lifetime account access Not available Not available
HR and Team Management
Manage and track time off Not available Included
Org charts Not available Additional fees
Document storage and audits Not available Additional fees
Custom onboarding workflows Not available Additional fees
Benefits and Compliance
Medical, dental, and vision plans Via SimplyInsured Additional fees
Integrated workers’ comp plans Additional fees Additional fees
Integrated 401(k) plan Pay premiums only Additional fees
Reporting and Usability
Payroll and employee reports Included Included
Real-time reporting filters Included Not available
Custom report designer Not available Additional fees

Compare support

Your payroll provider’s software should be backed by a reliable, easy-to-reach team of experts. We break down the level of support you can expect from QuickBooks and Paychex.

QuickBooks Payroll Paychex Flex
Setup and data migration Additional fees for customized setup Additional fees
Expert phone support Additional fees for extended support hours Included
Chat support Included Included
Accuracy guarantee Included Not available

Decide what payroll features you need

Every business has needs and specific requirements, so it’s important to choose the right provider that can accommodate you. Both QuickBooks and Paychex have a wide range of features that may be of use to you, but here are few things to consider when making your choice.


Full-service payroll: There are some payroll providers out there that are essentially just payroll calculators, but don’t handle employer and employee taxes, new hire reporting, or handle distribution of W-2s and 1099s. So, make sure to look out for a provider that will automate taxes on your behalf, and guarantees accuracy as well.


Both QuickBooks Payroll and Paychex offer full-service payroll, but you may be incurring some extra fees for standard services (like W-2 filing) from Paychex. And of the two providers, only QuickBooks provides an accuracy guarantee on your taxes. In the market, there are other providers that include both full-service payroll and an accuracy guarantee at no additional cost.



Specific industries: As mentioned before, every business has unique payroll requirements. They can change depending on industry, company size, location, and more. So, whether you’re a church with parsonage allowances, or a restaurant processing tips, your payroll provider should be able to handle those requirements for you, and ideally at no additional cost.


QuickBooks and Paychex both serve a wide range of businesses and industries, but costs vary depending on your requirements and company size. Review feature lists carefully to make sure all your needs are covered.



Integrations: Seamless integrations with other software and apps are also an important feature to look for. When data can flow freely between (for example) payroll, time-tracking and accounting solutions, it can help streamline your operations, save time, and reduce errors.


QuickBooks and Paychex are both equipped with a number of integration options for time-tracking and accounting software. However, Paychex charges additional fees for some accounting software integrations. QuickBooks Payroll includes integrations in its base price, and many business owners choose it under the assumption that it’s the best choice for integrating with QuickBooks Online and Desktop accounting software. In fact, other payroll providers offer more flexible QuickBooks integrations.



Reporting capabilities: Getting your payroll reports organized the way you want them to is essential. Depending on the ways you may be working with your accountant or other business partners, flexibility in reporting allows you to analyze expenses and make better business decisions.


While both QuickBooks and Paychex offer reports, the flexibility and customization options are quite limited. Some payroll providers offer built-in report designers that let you customize and filter the data in real time, then save custom reports. This way, you don’t have to spend time exporting and organizing reports in spreadsheets. If payroll reporting is important to you, it’s worth taking a close look at it.



Compare more providers

When choosing between QuickBooks and Paychex small businesses may see a set of services and functionality, but the price for both can vary, depending on the features you need. And other services offer more flexibility, a better value, and higher ratings and reviews. If you’re still looking for payroll options, try comparing all the top providers in one place:


See who's the top-rated provider

Or see how Paychex Flex and QuickBooks payroll do versus individual providers:

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