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.
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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.
QuickBooks Payroll
Ease of Setup
Ease of Admin
Quality of Support
Performance
Reliability
Customization
Reporting
Paychex Flex
Ease of Setup
Ease of Admin
Quality of Support
Performance
Reliability
Customization
Reporting
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 |
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 |
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.
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:
Or see how Paychex Flex and QuickBooks payroll do versus individual providers:
We’ll even migrate all your employee info and prior wages for you.