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Paychex Flex HR Software Review

Jeff Hale
Jeff Hale
Business News Daily Contributing Writer
Updated Nov 23, 2022
  • Paychex Flex human resources software provides all the tools to manage people across your company.
  • Paychex Flex can handle businesses’ payroll, benefits administration, hiring, onboarding, and time and attendance needs.
  • Businesses of any size can choose from three Paychex Flex plans.
  • This review is for business owners who are considering Paychex Flex for their HR software needs.

Paychex Flex is popular human resources software that can help nearly every business, from startups to enterprise-level businesses, with hiring, onboarding, employee benefits, time tracking, payroll, tax filing and compliance. The time-saving 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 capabilities, which are available through a mobile app. Paychex Flex is especially well suited for distributed workforces, with ample solutions to meet the needs of companies with remote employees.

Paychex company logo

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 Editor’s Score: 94/100

User interface90
Customer support95

Why Paychex Flex Is the Best for Remote Teams

Of the HR software providers we reviewed, Paychex Flex offered some of the most remote-friendly features, including paperless onboarding, e-learning courses for remote training, a user-friendly mobile app, and strong employee self-service features. Paychex Flex also automatically calculates payroll taxes for each employee based on their location, making it easier for employers to run payroll for remote employees distributed across different states. The regulatory tools are also helpful for employers that must juggle compliance requirements across different cities and states.


  • Paychex offers compliance, onboarding and payroll features that are well suited for organizations with remote staff.
  • The employee self-service features are very easy to use on both the mobile app and the web platform.


  • Paychex runs primarily on a custom pricing model, so you have to speak to a sales rep to get a quote.
  • There is no free trial. If you want to test HR software before committing to it, see our Zenefits review or BambooHR review to learn more about software platforms that offer free trials.

Paychex Flex Reporting

Paychex Flex offers a wide range of reporting and analytics tracking tools presented in a user-friendly dashboard. There is also an interactive chat assistant to help support administrators and employees. Credit: Paychex


We found Paychex’s user interface out of date compared with those of other HR software platforms we evaluated. However, if you’re transitioning from a spreadsheet or an accounting-oriented provider such as QuickBooks, you may feel right at home with the classic look and feel.

We like how the dashboard gives you instant access to your current and most recent payroll, as well as the total cash required for your upcoming payday deadline. Other areas, like the hiring tool, let you publish new job openings on career sites and social media pages. Once your company receives applications, the tool also makes it easy to objectively compare candidates with interactive analytics.

Did you know?Did you know?: Paychex Flex has 680,000 customers, making it one of the most widely used HR software platforms.

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 relying on a fully or partially remote workforce, the ability to access information and accomplish tasks from anywhere makes Paychex an attractive service.

Paychex Flex payroll

Users can access and run payroll reporting on their mobile devices with Paychex Flex’s Android and iOS apps. Credit: Paychex Flex (via Google Play)

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

Paychex Flex Features

Pay and deductionsAuto-calculate employee pay and deductions for health insurance and garnishments.
Payroll taxEasily manage and submit all of your payroll taxes and year-end W-2 and 1099 filings.
IntegrationsSync your payroll data with your existing accounting software programs, such as QuickBooks and Sage.
OnboardingUse digital onboarding tools for new hires, including I-9, withholdings and banking forms.
HR administrationTrack and store performance reviews, training tools and employee documents.
HiringRecruit 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 location-based calculations are helpful for managing payroll for remote staff who may have different minimum-wage laws and deductions for state-specific programs, like state disability. The system can also reconcile one-time bonuses, commissions and recurring wage garnishments whenever applicable.

Paychex Flex payroll tools

Paychex’s payroll tools allow employers to review upcoming payroll reports, individual paycheck details and the total cash amount needed for each payroll cycle. Credit: Paychex

Payroll Tax

Staying up to date with local, state and federal payroll taxes is another potentially troublesome area for businesses, especially remote businesses that have employees spread out across many regions. 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 there are mistakes, it takes care of tax penalties you may incur.


The Flex Select and Flex Enterprise plans offer the ability to securely link your company’s payroll data to many accounting software programs, including those in our QuickBooks review and Xero review. 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 Flex integrations

Paychex Flex offers a number of valuable integration options. Credit: Paychex


You can eliminate new-hire paperwork and provide your new team members with a positive user experience. Paychex Flex provides easy-to-complete digital forms, new-hire checklists and automated form collection, offering a completely paperless experience and the confidence of E-Verify solutions. The company offers tools for a fully paperless onboarding experience, which businesses will find useful when onboarding remote employees.

Paychex Flex onboarding

Paychex offers an onboarding checklist tool that simplifies the process for employees and the HR team. Credit: Paychex

HR Administration

The optional professional employer organization (PEO) 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 that use this add-on service can consolidate their buying power for benefits that are normally available only 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 save you 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 Flex Cost

Paychex offers three subscription options designed to fit the needs of small, midsize or enterprise-level businesses. The entry-level pricing, which starts at $39 per month plus $5 per person, is fairly transparent. For the Flex Select and Flex Enterprise plans, however, you will need to contact Paychex to get a quote.

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. Here is more information about each plan:

Paychex Flex Essentials

  • Pricing: Base price of $39 per month plus $5 per person per month
  • 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: Request a custom 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: Request a custom 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.

Did you know?Did you know?: You can also check out our Paychex time and attendance software review, Paychex payroll service review and Paychex HR outsourcing review to learn more about these services.

Paychex Flex Setup

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.

Paychex Flex 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. The Paychex team consists of more than 600 HR professionals who have an average of eight years of training and expertise. Paychex also employs more than 200 experts on compliance relating to federal, state and local regulations.

Flex Select and Flex Enterprise customers are assigned a highly trained, dedicated payroll specialist who serves as the key point of contact for help with tax or payroll needs. Paychex also maintains a self-guided library of useful how-to guides and tips that can improve your HR department’s operations.

Paychex Flex Drawbacks

One potential drawback of Paychex is that it is a sales-focused organization that does not provide much transparency about pricing for most of its products and services. That means you must request pricing information, and you may need to negotiate. Other providers in this space are more forthcoming with the cost of their services, and that transparency gives us more confidence when shopping and comparing service providers. See our Gusto review for an example of transparent pricing.

For the Paychex Flex Select and Enterprise plans, your total monthly cost 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.


We conducted comprehensive research and analyzed leading HR systems to identify the best HR software solutions on the market. We watched product videos and interactive product tours, as well as conducted demos and free trials whenever they were available. When looking for the best HR software for remote teams specifically, we prioritized features such as onboarding and implementation, payroll processing, benefits administration, usability, integrations, reporting and customer support.

Paychex Flex FAQs

What is the difference between Paychex and Paychex Flex?

Paychex Flex is Paychex’s all-in-one HR solution. The Paychex company also owns Paychex Oasis, a PEO service.

Is Paychex Flex free?

No, Paychex Flex does not currently offer a free plan.

Does Paychex Flex offer payroll support?

Yes, payroll is included with Paychex Flex plans, including the entry-level Paychex Flex Essentials plan. Higher-level plans include access to a dedicated payroll specialist for support as well.

Overall Value

We recommend Paychex for …

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

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.
Paychex company logo

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.