Paychex Flex Review
Visit Paychex Flex

Paychex Flex Review

Are you looking for a payroll application that can grow along with your business? If so, be sure to check out Paychex Flex, from industry leader Paychex. Created for small businesses with one to 49 employees, Paychex Flex offers four plans that can be custom designed to fit the needs of your business.

Quick Hits

What We Like

  • Scalable, with four plans available
  • All plans offer payroll tax administration
  • Excellent mobile app

Could Be Better

  • Confusing pricing
  • Employee onboarding only in top two plans
  • Limited integration capability

The Blueprint Score

Determined and ranked by our resident expert based on firsthand knowledge and unbiased research.

Ease of Use 8/10
Support 9/10
Pricing 7/10
Features 8/10
8.0 out of 10

We may receive compensation from partners and advertisers whose products appear here. Compensation may impact where products are placed on our site, but editorial opinions, scores, and reviews are independent from, and never influenced by, any advertiser or partner.

Updated June 4, 2020

Save as PDF

Paychex is a payroll software that was originally founded in 1971 as an alternative to payroll behemoth Run Powered by ADP.

Today, Paychex serves more than 670,000 users, and has grown to more than 100 locations nationwide. To better serve the small business community, Paychex created Paychex Flex, designed specifically for small businesses.

This payroll solution is scalable, with a variety of plans and add-on options available, all designed with the small business owner in mind.

Who is Paychex Flex for?

Paychex Flex is designed for businesses with fewer than 49 employees.

The application offers four plans to choose from.

Express Payroll is good for up to 10 employees, Paychex Flex Select is designed for between 10 and 49 employees, Paychex Flex Pro is a good fit for businesses with 50 or more employees, and Paychex Flex Enterprise, for businesses with more than 100 employees.

Out of these options, Paychex Flex Select is the most popular choice for small business owners.

With a really robust mobile app, Paychex Flex is also a good fit for business owners on the go, or those of you who use your phone to conduct business.

Paychex Flex’s features

The features available to you in Paychex Flex are entirely dependent upon the plan purchased.

Many of the more useful features, such as General Ledger Service, a Workers’ Compensation Report, State Unemployment Insurance, and Analytics and Reports, are only found in the more expensive Paychex Flex plans.

Fortunately, you do have the option to add these services to your Paychex Flex Select account, but they will increase the cost of the application. Contract employees can also be paid in Paychex Flex, with year-end W-2s and 1099s processed by Paychex Flex for a small fee.

Other features available in all plans include:

  • New-hire reporting
  • 24/7 phone and chat support
  • Automated employment and income verification
  • Paycards
  • Payroll available for all 50 states

In addition, Paychex Flex offers a variety of other services, including HR Records, Hiring and Onboarding, Time & Attendance, Recruiting & Applicant Tracking, Benefits Administration, and Reporting and Analytics.

However, the product offers limited integration options with third-party accounting or timekeeping applications,

Mobile app

Hands down, one of the best features in Paychex Flex is its mobile app. The mobile app provides access to many of the features found in the online application, including the user dashboard, where you can enter, review, and submit payroll information.

You can also access employee records, view benefits and retirement account activity, and view your last payroll from the mobile app.

Flexible pay options

All Paychex Flex plans offer free direct deposit for your employees, as well as an option to pay your employees with a pay card.

The Select, Pro, and Enterprise plans also offer paper checks, check signing services, and a check logo service.

Payroll tax administration

Most small business owners will tell you that the number one reason why they use a full-service payroll software is for calculating, filing, and paying payroll taxes.

No need to worry about that in Paychex Flex, as all four plans offer complete payroll tax administration as well as new-hire reporting, though the State Unemployment Insurance Service is only available in the Pro and Enterprise plans.

Employee self-service portal (Pro and Enterprise only)

While this is only available in the two most expensive Paychex Flex plans, it may be a good idea to purchase it as an add-on for the Select plan. The online portal lets you save a lot of time by having your employees complete the onboarding process, including filling out new hire documents such as a W-4 or I-9.

Paychex Flex workflow for new hires with a list of steps to complete

The Employee Self-Service option lets your employee access and complete a variety of forms.

Employees can also complete direct deposit information and later use the portal to access paystubs, change tax information, and check vacation and sick time balances.

Employees can also access the Paychex Learning Management System, an e-learning platform designed to educate and engage your employees, directly through the employee portal.


Optional in the Select plan, the Analytics and Reporting option provides you with access to more than 160 standard reports that are fully customizable. A Custom Analytics and Reporting option is available in the Enterprise plan if you need to create custom reports for your business, and can also be purchased as an add-on as well.

Additional services

In addition to full-service payroll, Paychex Flex offers a variety of other options that your small business may be interested in, including the following:

  • Time and attendance
  • HR services
  • Hiring services
  • Employee benefits
  • Business insurance
  • Finances and payments
  • Startup services

These services are all designed to integrate with the payroll application and will need to be purchased separately.

Paychex Flex’s ease of use

Paychex Flex offers easy system navigation from the user dashboard, which displays summary information such as Quick Reports, Current Payroll, and Last Payroll, along with access to frequently used functions that include adding an employee or viewing an employee list.

A vertical menu bar to the left of the screen gives you easy access to all features, including the payroll center, as well as any optional modules purchased.

Paychex Flex sample dashboard with cards for analytics and reports, feedback, current payroll, last payroll, and people

Paychex Flex’s customizable dashboard offers detailed payroll information.

Paychex Flex handles all initial product setup. Once set up, you can call into Paychex and submit your payroll information through their automated system or enter payroll data in the application. The payroll entry screen resembles a grid and is designed to make payroll entry quick and painless.

Here, you can choose to pay any or all of your employees, add hours worked for hourly employees, and add bonus information as well as vacation and sick pay hours.

Payrolls can be reviewed and edited before processing, and you can opt to automatically print payroll reports such as a payroll register or tax liability report after each payroll run.

Paychex Flex’s pricing

Paychex Flex does not publicly share pricing for its payroll services or other related features; potential users need to contact the company directly for pricing. Average pricing for a business with 10 employees is estimated at $3,000 annually, though Paychex Flex does offer a variety of discounts to first-time subscribers that would likely bring that number down.

However, multiple add-ons can quickly raise the annual cost of this application, and since Paychex Flex charges by payrun, you’ll also pay more for any extra payruns you have throughout the year.

Paychex Flex charges a $200 setup fee, and you’ll also pay an additional charge for year-end forms such as W-2s and 1099s.

Paychex Flex pricing chart

Paychex Flex is scalable, with four plans available.

Most of the features in the more expensive plans are also available in the Paychex Flex Select plan at an additional cost. You’ll also pay more if you add additional features such as Time and Attendance, HR, and Employee Benefit Administration.

Working with Paychex Flex support

Paychex Flex offers 24/7 phone and chat support, with separate support pages available for payroll administrators and employees.

You can also access Paychex Flex help from within the application. There are various ways to contact product support, including logging into the Paychex Flex support page to request assistance.

You can also use its toll-free number, or contact local support through the Paychex Flex support page. Select, Pro, and Enterprise users are also assigned a dedicated payroll specialist who will assist you with initial product setup and later serves as your single point of contact for any payroll or tax issues that may arise.

Benefits of Paychex Flex

One of the biggest benefits to using Paychex Flex is the availability of complete payroll tax administration in all four plans, giving even the smallest business access to complete payroll tax filing and remittance.

Another benefit is the ability to scale up to a more robust plan, or even just add a few of the services you desire to your current plan. However, this same flexibility can be expensive, and those on a tight budget may be better served by a product with a different pricing structure.

Other benefits include the comprehensive mobile app available for Paychex Flex, which allows you to perform all of your necessary payroll functions from your smartphone.

Is Paychex Flex the solution for your small business?

Paychex Flex could be a great right payroll application for your business. All four pricing plans offer easy online payroll preparation, free direct deposit, and complete payroll tax administration.

There is also a long list of add-on options available for businesses to choose from, and support options are solid. However, Paychex Flex’s a-la-carte menu can become very expensive very quickly, so smaller businesses with tighter budgets may want to look at a more inclusive application.

Frequently Asked Questions

Will Paychex Flex take care of my payroll taxes?

Yes, all Paychex Flex plans include complete calculation, filing, and tax remittance service.

Can I pay employees in more than one state?

Yes. Paychex Flex offers payroll services for all 50 states.

Does Paychex Flex offer a mobile app?

Paychex Flex’s mobile app is one of the best to be found in payroll applications, allowing you to enter payroll information and review and run payroll directly from your smartphone.

With Paychex Flex, growth doesn't mean switching payroll software.

With Paychex Flex, growth doesn't mean switching payroll software.

How Paychex Flex Compares

Online access Direct deposit Prepares federal tax forms Employee access to payroll documents
Paychex Flex
QuickBooks Payroll
Payroll Mate