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Paychex Flex HR Software Review

Jeff Hale
Jeff Hale
  • Paychex human resources software provides all the tools businesses need to manage people across your company.
  • The software can handle all of your payroll, benefits administration, hiring, onboarding, and time and attendance needs.
  • Businesses of any size can choose from three Paychex Flex plans for their HR needs.
  • This review is for business owners who are considering implementing Paychex Flex for their HR software needs.

Paychex is a popular human resources software solution that can help nearly every business, from startups to enterprise-level businesses, with its hiring, onboarding, employee benefits, time-tracking, payroll, tax filing and compliance needs. Its timesaving platform automatically calculates, pays, and files your state and federal payroll taxes, as well as most local payroll taxes. Mid- and top-tier plans give your employees a range of self-service actions, which are available through a mobile app. Paychex is especially well suited for work-at-home operations, with ample solutions to meet the needs of companies relying on remote employees and teams.

Paychex Flex HR Software

Paychex Flex HR Software

The Verdict

Paychex is great for businesses with remote teams looking for an all-in-one solution with desktop and mobile access to payroll, benefits, and HR compliance.

Paychex Flex HR Software Pricing

Paychex offers three subscription options designed to fit the needs of small, midsize or enterprise-level businesses. The entry-level Go pricing that starts at $59 per month is fairly transparent. You will need to contact Paychex about its rates for the Flex Select and Flex Enterprise options.

Add-ons for accounting software integration, time tracking and attendance, and additional employee pay options, including paper checks, check signing, and a check logo service, are available for an extra fee.

Paychex Go

  • Pricing: Base price of $59 per month plus $4 per month per person
  • Standout features: Online payroll, payroll tax administration, new-hire reporting, general ledger report, standard analysis and reporting, direct deposit and/or pay cards, automatic W-2s and 1099s, and U.S.-based customer service

Paychex Flex Select

  • Pricing: Customized; call for quote
  • Standout features: Mobile app functionality, integrations with many third-party tools, $1,000 in prepaid digital marketing services, dedicated payroll specialists, employee financial wellness tools and 24/7 employment income verification services

Paychex Flex Enterprise

  • Pricing: Customized; call for quote
  • Standout features: Accounting software integration, workers' compensation reports and payment services, state unemployment insurance services, custom analytics and reporting, garnishment payment services, onboarding essentials, and employee screening

In addition to these three standard plans, Paychex offers custom solutions based on your business's size; these services are designed to help you comply with various regulations and stay in control of your HR infrastructure.


We found the overall user interface with Paychex to feel out of date compared to other providers we evaluated. However, if you're transitioning from a spreadsheet or an accounting-oriented provider such as QuickBooks, then you may feel right at home with the classic look and feel of Paychex's interface. We like how the dashboard gives you instant access to your current and most recent payroll, along with the total cash required for your upcoming payday deadline. Other areas, like the "hiring" tool, let you publish new job openings to career sites and social media pages. Once your company receives applications, the tool also makes it easy to objectively compare candidates with interactive analytics.

Key TakeawayKey takeaway: Paychex has more than 160 helpful reports, with customizable options that put the data that's most important to you in front of you and your administrators.

The Paychex Flex dashboard provides a quick overview of your payroll status and tasks that need completing.

Paychex users have the option to run payroll from any computer or handheld device. The mobile-friendly software also allows administrators to import data, edit individual checks, review financial information and access valuable reports in multiple formats. With many businesses across the country still relying on a fully or partially remote workforce, the ability to access information and accomplish tasks from anywhere makes Paychex an attractive service.

Did you know?Did you know? The cloud-based platform is utilized by 680,000 customers, making it one of the largest in the industry.

For Flex-level subscribers, employees can use Touch ID and/or Face ID to access their pay stubs, W-2s, 401(k) balances, and health-related benefits from the mobile app.

The Paychex mobile app gives users access to their payroll and benefits information instantly.

Paychex Flex HR Software Features

Pay and deductions Auto-calculate employee pay and deductions for health insurance and garnishments.
Payroll tax Easily manage and submit all of your payroll taxes and year-end W-2 and 1099 filings.
Integrations Sync your payroll data to your existing accounting software programs, such as QuickBooks and Sage.
Onboarding Use digital onboarding tools for new hires, including I-9s, withholdings and banking forms.
HR administration Track and store performance reviews, training tools and employee documents.
Hiring Recruit and verify an applicant's identity, criminal activity, education and professional licenses.

Pay and Deductions

Paychex simplifies the process of running payroll and reduces the risk of costly mistakes. The intuitive software automatically calculates the wages for each employee based on their location, pay rate and hours worked. The system can also reconcile one-time bonuses, commissions and recurring wage garnishments whenever applicable.

Payroll Tax

Staying up to date with local, state and federal payroll taxes is another potentially troublesome area for businesses. Paychex calculates, files and pays all of your payroll taxes on your behalf. Additionally, the company files all of your W-2 or 1099 forms accurately and on time. If mistakes are made, it takes care of tax penalties you may incur.


The Flex Enterprise and Go plans offer the ability to securely link your company's payroll data to many accounting software programs, including QuickBooks, Sage and Xero. Other integrations allow you to share data between Paychex Flex and dozens of your existing HR, point-of-sale, productivity, and other third-party tools.

Paychex offers a number of valuable integration options.


You can eliminate new-hire paperwork and provide your new team members with a positive user experience. This includes easy-to-complete digital forms, new-hire checklists, and automated form collection, with a completely paperless experience and the confidence of E-Verify solutions.

HR Administration

The optional professional employer organization platform offers services from highly experienced HR professionals who can proactively address key areas of risk and guide you through OSHA regulations, state unemployment insurance administration, payroll processing, and health benefits enrollment. Businesses using this add-on service can consolidate their buying power for benefits that are normally only available to much larger organizations.


Paychex's optional hiring integration helps companies recruit, screen and hire applicants from one simple dashboard. Optional services such as background checks and drug testing can help you save time as you screen candidates. The long list of talent-acquisition tools can assist your HR administrators in verifying candidate qualifications, reducing employee turnover and minimizing potential claims of poor or illegal hiring practices.

Paychex's hiring tools allow you to easily view those who have applied for open positions within your company.


You can expect to be up and running with Paychex in as little as 48 hours from the time you sign up for one of its plans. Paychex customer service agents will work with your team to collect all of the required paperwork to set up your year-to-date payroll data.

Depending on which payroll service provider you are switching from, Paychex may even be able to assist you in transferring old data from your previous system. Once Paychex has reviewed your application and information, you can run your first payroll.

Customer Service

Your administrators and employees will be able to reach a member of Paychex's U.S.-based customer service team by phone, chat or online form 24/7. According to the company, its team consists of more than 600 HR professionals who average eight years of training and expertise. Paychex also employs more than 200 compliance experts relating to federal, state and local regulations.

Customers with Flex Select and Flex Enterprise are assigned a highly trained, dedicated payroll specialist who serves as the key point of contact for help with tax or payroll needs.

TipTip: You can use Paychex's online self-help resource center for everything from navigating COVID-19 to reviewing frequently asked questions about using the latest features.


Paychex is a sales-focused organization without much transparency about pricing for most of its products and services. That means you will need to request pricing, and you may need to negotiate with the company. Other competitors in this space, such as Gusto, are more forthcoming with the cost of their services, which tends to give us more confidence when shopping and comparing service providers.

Your total monthly cost for Paychex Flex Select and Enterprise plans is based on how often you run payroll. If you employ both hourly workers and salaried staff, your costs can add up quickly. For example, if you run payroll for your salaried staff biweekly, pay your hourly workers on the same schedule and run a one-time bonus payroll for your top salespeople, you'll incur costs for five separate payroll runs in one month. If you need to correct any errors along the way, that also counts as an additional payroll run. We recommend that you tell the Paychex sales agent how often you typically run payroll so you get an accurate quote and aren't hit with surprise fees after you sign up for the service.


Who we recommend Paychex for:

  • Large businesses with remote teams looking for an all-in-one solution with desktop and mobile access to payroll, benefits, and HR compliance
  • Small and midsize businesses that want to help finding and hiring the best people for the job
  • Any business looking for a simple, accounting-focused, all-in-one HR platform

Who we DON'T recommend Paychex for:

  • Companies that value a clean interface and modern user experience when managing employee payroll, HR, time and attendance, health and benefits, and retirement services
  • Business owners who appreciate transparent pricing and do not want to negotiate with a sales representative for standard service packages or add-on features

Image Credit: fizkes / Getty Images
Paychex Flex HR Software

Paychex Flex HR Software

The Verdict

Paychex is great for businesses with remote teams looking for an all-in-one solution with desktop and mobile access to payroll, benefits, and HR compliance.

Jeff Hale
Jeff Hale
Business News Daily Contributing Writer
Jeff Hale is a writer and editor based in San Diego with a background in business development and marketing. He has identified new market opportunities for Fortune 500 companies and developed communications strategies and digital branding for tech startups and small businesses. Jeff covers emerging technologies and business solutions with a focus on efficiency and growth. He holds a Bachelor’s degree in English from the University of California, Irvine, and an MBA from Chapman University.