Paychex vs QuickBooks Comparison

Payroll is an absolutely crucial business process, and because it’s often complex and tedious many entrepreneurs rely on a professional payroll service to do the job. 

Two of the leading online services to consider are Paychex and QuickBooks. To help you determine which is better, and which might be best for you and your business, we have thoroughly reviewed their services by putting ourselves in the shoes of an entrepreneur. 

Read on to make the choice that will keep your business on the surest path to success. 

Pros and Cons

Paychex

QuickBooks

Features and Services Overview

Paychex has three plans. Their base plan offers a full suite of payroll services including tax filings. Their middle plan offers everything in the base plan plus the Paychex learning management system.

Their top-tier plan includes a dedicated payroll specialist, accounting integrations, and employee screening and onboarding tools.

QuickBooks also has three plans, all of which include multi-state payroll services. Their plans include healthcare and 401K administration. 

Plans Pricing

The Paychex top-tier plan also has custom pricing and offers a dedicated payroll specialist and accounting integrations. 

The QuickBooks base plan is $45 per month plus $5 per employee per month. It offers full-service payroll including W-2s and 1099s and tax filings. It also includes health insurance and 401K administration.

QuickBooks’ middle plan is $75 per month plus $8 per employee per month. It offers same-day direct deposit, as opposed to next-day in the base plan. It also includes time tracking on the go, which allows you to track and approve an employee’s hours from a mobile app. 

With the plan, you’ll also have access to an HR support center and receive workers’ compensation administration. 

QuickBooks’ top-tier plan is $125 per month plus $10 per employee per month and provides the unique benefit of tax penalty protection. If your business is fined for late tax filings, Quickbooks will cover the fee up to $25,000, subject to terms and conditions. You’ll also have a personal HR advisor. 

Paychex Flex Essentials vs Core Plan

The Paychex plan is less expensive and offers many extras but does not include employee benefits like the QuickBooks plan does.

	Paychex	QuickBooks
Price	$39 per month plus $5 per employee per month	$45 plus $5 per employee per month
Payroll service	Included	Included
Direct Deposit and on site check printing	Included	Included
Mobile app for employers and employees	Included	Included
Analytics and reporting	Included	Reporting only
Garnishments	Included	Not included
W-2s and 1099s	Included at an additional cost	Included
New Hire reporting	Included	Not included
Customer Support	Included	Included
Labor compliance poster kit	Included	Not included
Worker’s compensation administration	Included at an additional cost	Not included
HR library and business forms	Included	Not included
401K plans	Not included	Included
Health care benefits	Not included	Included

Paychex Flex Select Plan vs Premium Plan

Again, Paychex does not include employee benefits, but does offer a learning management system. The QuickBooks plan also includes workers’ compensation administration at no additional cost. 

	Paychex	QuickBooks
Price	Custom pricing	$75 plus $8 per employee per month
Payroll service	Included	Included
Direct Deposit and on site check printing	Included	Included
Mobile app for employers and employees	Included	Included
Analytics and reporting	Included	Reporting only
Garnishments	Included	Not included
W-2s and 1099s	Included at an additional cost	Included
New Hire reporting	Included	Not included
Customer Support	Included	Included
Labor compliance poster kit	Included	Not included
Worker’s compensation administration	Included at an additional cost	Included
HR library and business forms	Included	Included
401K plans	Not included	Included
Health care benefits	Not included	Included
Learning management system	Included	Not included

Paychex Flex Pro Plan vs Elite Plan

The Paychex plan offers a richer suite of payroll and HR services, but QuickBooks still has the advantage of employee benefits.

	Paychex	QuickBooks
Price	Custom pricing	$125 plus $10 per employee per month
Payroll service	Included	Included
Direct Deposit and on site check printing	Included	Included
Mobile app for employers and employees	Included	Included
Analytics and reporting	Included	Reporting only
Garnishments	Included	Not included
W-2s and 1099s	Included at an additional cost	Included
New Hire reporting	Included	Not included
Customer Support	Included	24/7
Labor compliance poster kit	Included	Not included
Worker’s compensation administration	Included at an additional cost	Included
HR library and business forms	Included	Included
401K plans	Not included	Included
Health care benefits	Not included	Included
Learning management system	Included	Not included
Guided setup	Included	Not included
Dedicated payroll specialist	Included	Not included
Personal HR advisor	Not included	Included
Accounting software integration	Included	Not included
State unemployment insurance services	Included	Not included
Onboarding	Included	Not included
Employee screening	Included	Not included
Tax penalty protection	Not included	Included

Paychex Website Interface and Navigation

The site is user-friendly. The plans are easy to find, with good detail on included features. You can even get more information on each individual service. It’s laid out well and easy to understand. 

Pricing is a bit trickier to navigate, as you must submit a quote to obtain the cost of both the Select and Pro plans. The site also has a robust help center where you can get information on a variety of topics.

How’s the signup process navigation?

While you’re unable to sign up for the Select and Pro plans without contacting a representative and obtaining a quote, you can go ahead and register for the base Essentials plan. 

To start the signup process for the Flex Essentials plan, click Sign Up Online. The next screen will prompt you to enter your contact information. There’s also an informative video about the plan on the right side of the page, along with a summary of the plan’s benefits.

Next, enter your company information and EIN. 

Next, confirm your plan selection, and you’ll be reminded that you won’t pay anything until your first payroll run. 

You will also get to see a cost breakdown before finalizing your choice.

The last step asks if you’d like to sign up for free services from third-party providers.

Make your selections and then click Complete Sign Up at the bottom of the screen.

How’s the mobile experience?

The Paychex Flex platform is extremely mobile-friendly, with several apps available for both employers and employees. When you sign up for a Paychex Flex account, you get access to the Paychex Flex App. 

This app connects employers to vital payroll and benefits features with the security of Touch-ID and Face ID authentication. The Paychex Flex App also allows employers to enter, review, and submit payroll and access employee data and reports, while employees can access and update their own information.

Other available apps are tied to different Paychex solutions, such as timekeeping and employee benefits.

In Summary

Overall, the Paychex website is extremely user-friendly, with easy to follow navigation and a seamless sign-up process for the Essentials plan. Information about each plan is easy to find and explained in great detail. 

There are also informative videos throughout the website to further explain plans and benefits. The only downside was that pricing for both the Select and Pro plans is custom, and thus not readily available. But there are several opportunities to request a quote.

Paychex Customer Support

We tested all three forms of Paychex Flex customer support, as detailed below.  

Chat support

We probed a bit further and were able to start chatting with a live agent. We asked about the cancellation policy and they said we could get that information from the sales team. We asked if there was a chat feature available to speak with the sales team, and the agent said “not that I know of” and asked for our first and last name to have someone reach out to us. 

We closed the chat session without receiving an answer to our question.

Email support

Phone support

QuickBooks Website Interface and Navigation

The site is user-friendly. The plans are easy to find, with good detail on features and pricing. You can even get more information on each individual service. It’s laid out well and easy to understand.

How’s the signup process navigation

When you view all the packages, you’re advised to select one to set up an account. After you select your plan, you’re offered bundled plans that include QuickBooks accounting features. You can select one of those plans, or select “just payroll”. 

Then you go to check-out, where you’ll set up your account and password. The next step is to enter credit card information, which is unusual, as most competitors do not charge clients until the first payroll run. 

This means that with Quickbooks you need to be absolutely certain of your choices when you’re setting up your account. 

How’s the mobile experience?

QuickBooks has a robust mobile app for employers. You can enter employee hours, submit payroll, view payroll taxes and forms, and even pay payroll taxes. They also have an app for employees to track their hours and clock in or clock out. 

Th employers’ app is far superior to those of competitors. Many payroll services do not even have an app for employers to manage payroll. 

In Summary

The site is quite user-friendly and information is easy to find. The only issue was that new clients must pay immediately when they sign-up, which seems a bit aggressive. Otherwise, the site is not very “salesy” and just guides visitors to the optimal plan. Overall, a pleasant customer experience.

QuickBooks Customer Support

We tested all three forms of QuickBooks customer support, as detailed below.  

Chat support

Phone support

Email support

Verdict

After a thorough assessment, we have determined that Paychex offers the better value and broader service offerings. With Paychex you’ill save money and get more robust HR support. The main advantage of QuickBooks is the employee benefits they offer, but we feel that Paychex counters that with a stronger overall experience. 

Our approach

As a leading human resources advisory site, we take our responsibilities seriously. We understand that countless entrepreneurs, and potential entrepreneurs, rely on our judgments and insights, particularly when it comes to managing their business.

As a result, our writers do their utmost to gain a comprehensive understanding of the services offered and the actual customer experience. In this case, we:

• Examined every single page of both the Paychex and QuickBooks websites
• Reviewed all of their offerings
• Put ourselves in the customer’s shoes, creating accounts
• Communicated with customer service via chat, email and phone
• Gained a full understanding of the customer experience and service value

Thanks to this full immersion in the actual customer experience, our reviewer and team are able to provide the most complete and insightful comparison of Paychex and QuickBooks payroll services.