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 Paychex Flex and QuickBooks Payroll, and which ones you may have to pay a little extra for.
| Paychex Flex | Quickbooks Payroll | |
|---|---|---|
| Pricing | ||
| Monthly fee | No published price. Negotiate with sales. Price is per pay run. | Starting at $50 per month + $6.50 per person |
| Setup and data migration | Additional fees | Additional fees for customized setup |
| Full-service payroll | ||
| Automated federal, state, and local tax filings and payments | Included | Included |
| Unlimited pay runs | Additional fees | Included |
| Multi-state payroll | Additional fees | Included |
| 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 | Additional fees for some integrations | Included |
| New hire reporting | Included | Included |
| Year-end filings, W-2s, and 1099s | Additional fees | Additional fees |
| Accuracy guarantee | Not available | Included |
| Onboarding and Employee Self-Service | ||
| Employee self-onboarding | Additional fees | Included |
| 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 | Included | Not available |
| Org charts | Additional fees | Not available |
| Document storage and audits | Additional fees | Not available |
| Custom onboarding workflows | Additional fees | Not available |
| Benefits and Compliance | ||
| Integrated workers’ comp plans | Additional fees | Additional fees |
| Medical, dental, and vision plans | Additional fees | Via SimplyInsured |
| Integrated 401(k) plan | Additional fees | Pay premiums only |
| Customer support | ||
| Expert phone support | Included | Additional fees for extended support hours |
| Chat support | Included | Included |
*Based on 2024 client survey
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We’ve collected reviews from both Paychex Flex and QuickBooks Payroll clients as well as industry experts. Take a look at how small businesses and experts compare Paychex Flex and Quickbooks Payroll:
Customer review data on this page is all from G2.com. Links and additional resources.
Try OnPay out yourself to see how easy payroll and HR can be. To get started, just share a few basic details about your business. Our team of pros will set everything up and import your employees’ information for you.
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.
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.
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.
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.
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.
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