Paychex Flex Review

Paychex Inc.
Paychex Flex
Paychex Inc.
Rochester, NY
Deployment Model:
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Paychex Flex At A Glance

Good: Streamlined processes, dedicated support experts to help businesses navigate complex issues, flexible paycheck options.
Bad: Some users have experienced a steep learning curve and have mentioned the interface is outdated.
Bottom Line: Cloud-based software that empowers small and medium-sized companies to improve their productivity and grow their business.

Product Overview

Paychex Flex is cloud-based payroll software that helps small and medium-sized businesses streamline their payroll processes. Administrators can run payroll in two clicks, even while on the go. Employees can see their paystubs and make changes to their personnel info without HR’s involvement.

Paychex Flex integrates with Paychex Flex Time, a time and attendance software, which eliminates manual data entry.

The software has three packages clients can choose from based on their needs:

  • Paychex Flex Essentials – Paychex Flex Essentials is intended for small businesses and includes features, such as online payroll, tax administration, direct deposit, check printing, a mobile app, new-hire reporting, employee self service, employee financial wellness tools, standard reporting and analytics templates, garnishment payment services, automatic W-2 and 1099 forms, HR and business forms, employee onboarding and a labor compliance poster kit. Paychex offers these features at an additional cost: paycheck preview and approval, recruiting, performance management, pre-employment screening, document management, time and attendance, API integration, business insurance, retirement services and employee benefits.
  • Paychex Flex Select – Paychex Flex Select includes all of the features of the Paychex Flex Essentials package, plus a learning management system.
  • Paychex Flex Pro – Paychex Flex Pro includes all of the features of the Paychex Flex Select package, plus a general ledger service, integration with general ledgers in accounting software, state unemployment insurance services, workers’ compensation payment services, pre-employment screening and an employee handbook builder.


Here are some key features of Paychex Flex:

Payroll processing – In the Payroll Center, administrators can run payroll and customize any earnings and deductions. With the dashboard, they can see their payroll journal, check stubs, cash requirements and other important information at a glance. The software has built-in safeguards to ensure payroll runs are accurate, including notifications of discrepancies in the data. Paychex Flex has multiple pay options for employers, such as direct deposit, check printing and paycards.

Tax management – Paychex Flex provides employers with automatic federal, state and local payroll tax calculations, filing and payment. In addition, it provides W-2 and 1099 forms to employees and contractors. Paychex Flex can help businesses claim tax credits (e.g., Work Opportunity Tax Credits, location-based credits) by identifying and automatically applying for them, and it also reports new hires to the appropriate government agencies.

Reporting and analytics – The software has over 160 standard reports on various metrics. Administrators can quickly find specific reports in the All Reports tab, as well as save their commonly-used reports in their Favorites list. As mentioned, the Paychex Flex Enterprise package provides custom reports and analytics, so administrators can create reports using custom parameters.

Benefits administration – The vendor offers integrated employee benefits tools, such as health insurance plans, retirement plans, health savings accounts and Section 125 tax-saving cafeteria plans. Employees can enroll in and keep track of their benefits plans with the Paychex Flex mobile app. In addition, Paychex Flex offers a financial wellness program that coaches employees on managing their debt and expenses.

Other payroll services – Paychex provides additional payroll and tax services, such as an employment verification service, wage garnishments, workers’ compensation programs and a state unemployment service. Clients can also receive federal and state labor compliance posters to display in their office.

HR features – Even though Paychex Flex is well known for its payroll features, it integrates with other tools to provide users with a complete HR system. Those tools include a learning management system with built-in and custom courses, a new-hire onboarding module, background check features and performance management functionality.

Target Market

Paychex Flex targets small and medium-sized businesses in many industries. We’ve listed 10 of its clients below.

  • FunnelBox Inc.
  • ESET North America
  • The Accounting Office Inc.
  • Industrial Manufacturing Solutions
  • Smile Cafe
  • Cottrell Paper Co.
  • Crown Jewell Entertainment
  • The American Society of Tropical Medicine and Hygiene
  • Pet Partners
  • Coronado Brewing Company

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New clients can access their account within a few days once Paychex receives the information needed for account setup (e.g., bank accounts, employer identification numbers, employee email addresses). If a client is switching from another payroll software, Paychex can import that data directly from the software.

As part of account setup, the implementation specialist balances year-end data and processes the first few payroll runs. The specialist will also provide training on the system, including how to process payroll, generate reports and give self-service access to employees.

Paychex Flex integrates with third-party software, such as accounting solutions, HRMS software, time and attendance systems and point of sale (POS) systems.

Customer Service & Support

Administrators can reach Paychex’s U.S.-based customer support team by phone, email or chat. Employees can browse the Frequently Asked Questions (FAQs) bank or click on the Help icon within their account.

In addition, Paychex Flex Select and Pro package users are assigned a dedicated payroll specialist for payroll and tax questions.


The Paychex Flex Essentials package costs $39 per month, plus $5 per employee, per month.

Pricing for Paychex Flex Select and Pro packages aren’t publicly available. Contact the vendor directly for a quote.


Some users have experienced a challenging learning curve with Paychex and have said the interface has an outdated look.


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Paychex is a leading provider of integrated human capital management solutions for payroll, benefits, human resources and insurance services. By combining its innovative software-as-a-service technology and mobility platform with dedicated, personal service, the vendor empowers small and medium-sized organizations to focus on their business’ growth.

Founded in 1971, Paychex serves approximately 730,000 payroll clients across more than 100 locations in the U.S. and Europe.

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