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Quickbooks Payroll vs Paychex Flex

Find out how these two payroll providers compare when it comes to pricing and features, including the latest ratings and reviews:

Quickbooks Payroll vs Paychex Flex:
Compare ratings and reviews

We’ve collected reviews from both Quickbooks Payroll and Paychex Flex clients as well as industry experts. Take a look at how small businesses and experts compare Paychex Flex and Quickbooks:

Paychex Flex

QuickBooks Payroll

Ease of Setup

8.4
7.9

Ease of Admin

8.6
8.1

Quality of Support

8.5
7.5

Performance

8.7
Not available

Reliability

8.9
8.9

Customization

7.7
Not available

Reporting

8.5
Not available

Ease of Setup

Paychex Flex

8.4

QuickBooks Payroll

7.9

Ease of Admin

Paychex Flex

8.6

QuickBooks Payroll

8.1

Quality of Support

Paychex Flex

8.5

QuickBooks Payroll

7.5

Performance

Paychex Flex

8.7

QuickBooks Payroll

Not available

Reliability

Paychex Flex

8.9

QuickBooks Payroll

8.9

Customization

Paychex Flex

7.7

QuickBooks Payroll

Not available

Reporting

Paychex Flex

8.5

QuickBooks Payroll

Not available

Customer review data on this page is all from G2.com. Links and additional resources.

Quickbooks Payroll vs Paychex Flex: 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 PayrollPaychex Flex
Pricing
Base priceTiered pricing, starting at $45 per monthNo published price. Negotiate with sales. Price is per pay run, not monthly.
Per worker cost Tiered pricing, starting at $4 per personNo 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 Additional fees for some integrations
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
Customer support
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

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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.

  • What full-service payroll features should I expect?

    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.

  • Do I have special payroll requirements for being in a certain industry?

    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.

  • What integrations are available?

    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.

  • What kind of payroll reporting is included?

    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.