Paychex Payroll Review: Pricing, Features, Alternatives

Updated on October 28, 2020
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    Paychex provides a full-service payroll solution for businesses of all sizes. It also offers a variety of other human resources services, including time and attendance management, benefits administration, hiring and compliance services, insurance, and professional employer organization (PEO) services.

    With so much to offer, Paychex has become one of the largest payroll service providers in the United States, with over 650,000 clients. If you’re a small business owner looking for a payroll service provider, you should consider Paychex—and we’re here to help.

    What Is Paychex Payroll?

    Paychex offers a payroll product for small businesses as well as midsize and large businesses. In this review, we’re going to focus on their small business product—Paychex Flex Select, which is designed for businesses with 10 to 49 employees.

    Flex Select is primarily a payroll service, but it sprinkles in some HR features as well. The system is cloud-hosted and accessible via the Paychex mobile app or by logging into your account from any internet-enabled device.

    With Paycheck Flex Select, you can run your payroll quickly and easily—in as little as two clicks—but built-in safeguards help ensure your payroll is accurate every time. Paychex also offers an employee portal so your employees can view their pay stubs and other applicable information. As an employer, you can also run over 160 reports and dashboards to gather any payroll-related data for your business.

    Paychex Cost

    Paychex does not list any specific pricing information on their website. Instead, everything is quote-based. This makes sense, considering you can do so much mixing and matching with Paychex’s different services. We’ll go over the four different payroll packages Paychex offers, but know that all of these can be customized with other HR services to match your business’s needs.

    Paychex Plans and Features

    Express Payroll Paychex Flex Select Paychex Flex Pro Paychex Flex Enterprise
    Best For
    Very small businesses looking for the essentials only
    Recommended for small businesses
    Businesses looking for more functionality, like onboarding and reporting features
    Recommended for enterprise-level businesses
    Employer Features
    -Payroll tax administration
    -New-hire reporting
    -Mobile app
    Labor compliance poster kit
    -General ledger service
    -Workers compensation report
    -State unemployment insurance service
    -Analytics and reporting
    -Garnishment payment service
    Custom analytics and reporting
    Employee Features
    -Financial wellness program
    -Direct deposit or paycards
    -Employment and income verification services
    -Additional employee pay options (paper checks, check signing, check logo service)
    -Paychex learning management system
    -Onboarding essentials
    -Employee screening essentials
    HR administration
    Customer Support
    24/7 phone and chat support
    -24/7 phone and chat support
    -Dedicated payroll specialist
    -24/7 phone and chat support
    -Dedicated payroll specialist
    -24/7 phone and chat support
    -Dedicated payroll specialist

    Since pricing is quote-based, we’d recommend calling Paychex and speaking with a sales representative to answer: how much is Paychex Payroll? Typically, payroll prices are determined based on how many employees you have, how often you run payroll, and the different services you are interested in using. Note that Paychex does advertise three free months of service for new users.

    Request a Free Quote From Paychex

    Paychex Features

    With this overview in mind, let’s take a closer look at some of the standout features that the Paychex system offers.

    Tax Administration and Compliance

    Every time you run payroll, Paychex will automatically calculate, pay, and file your payroll taxes with the appropriate federal, state, and local agencies based on the information you provided during onboarding. You can also file all new-hire documents through the Paychex system, including W-4s, I-9s, and state withholding forms. Flex Select customers also get free labor law compliance posters and wage garnishment assistance.

    For an additional annual fee of $99 you can sign up for Paychex Promise, a system that safeguards against payroll interruptions. With Paychex Promise, you can extend the collection of payroll funds from your bank account by up to seven days without interruption of services or insufficient fund charges. Other perks include the ability to run two same-day ACH deposits annually in instances where you are late to process payroll or need to correct a payment. Paychex Promise customers also have their payment history sent to credit bureaus to help them build business credit, receive access to a payroll fraud hotline, and can get lending options and financial health monitoring through Biz2Credit.

    Employee Self-Service

    Paychex Flex Select provides an online portal your employees can access to complete new hire paperwork and onboarding, access and change their personal information, fill out tax forms, view payroll data, request vacation, and check time-off balances.

    Employees also have access to an e-learning platform through their online portal with courses and tools on financial wellness, workplace productivity, time management skills, and more.


    Flex Select users can gain access to workforce analytics—a reporting suite with over 160 preset reports, including your payroll journal, cash requirements, and tax deposit notices. Reports are updated in real-time and can be viewed per pay period, quarter, or by a unique time range. You can also build custom reports and export your reports via a variety of formats.

    Additional Features

    On top of what comes with Flex Select, there are a variety of features you can add to your plan for an additional fee. Among your options is a general ledger service that allows you to link your Paychex account to your accounting software, workers compensation reports, unemployment insurance assistance, more in-depth reporting tools, a limited number of free employee background checks, and HR administration—including a performance feedback portal and document library where you can store training and compliance materials accessible to all your staff.

    HR Add-Ons

    As we mentioned, Paychex provides a variety of HR services on top of its payroll offering. Here is a list of other services Paychex provides:

    • Online timekeeping
    • Time clocks using biometric-identification
    • Benefits administration
    • Records administration
    • Hiring services
    • Employee onboarding
    • Employee screening
    • Recruitment and applicant tracking
    • Group health insurance
    • Individual health services
    • Retirement planning
    • Workers compensation
    • Business insurance
    • Business owner policy insurance
    • Commercial auto insurance
    • Liability insurance
    • Umbrella insurance
    • Business loans
    • Payment processing
    • Incorporation services
    • Online marketing services
    • PEO

    While the payroll plans are sold as individual packages, Paychex also allows customers to mix-and-match services to make a plan that works best for their business. For example, a small business owner can get their payroll, benefits administration, and recruitment and applicant tracking services from Paychex. Paychex also offers specific packages based on business size and role.

    Paychex Payroll Pros and Cons

    Given everything we have gone over, here is where Paychex stands out—and where it falls short.

    Paychex Pros

    • Scalable: Paychex’s variety of services combined with the option to add services to your plan as you grow makes Paychex a highly scalable option for small businesses. You can start out with just a basic payroll service and add on additional HR tools as needed.
    • Support: Setting up payroll can be confusing considering all the tax information and number crunching involved. That’s why it’s nice that Paychex gives you a dedicated account manager to help you every step of the way. That’s not something you see with every service provider.

    Paychex Cons

    • Ease of use: Given that Paychex is such a large platform that can provide services for many different business functions, some users found it difficult to learn and start using. Things users found confusing included processing payroll, setting up benefits, completing online forms. Some also said Paychex’s clunky UI made navigating the website confusing.
    • Price: Paychex’s lack of price transparency is a downside to consider, as well. While this allows businesses to create a totally custom solution that fits their business perfectly, it also means you can’t be sure that you’re getting the best price. We recommend getting quotes from several payroll providers and comparing your options before you make a final decision.

    How Does Paychex Payroll Work?

    As some user reviews noted, Paychex isn’t the easiest solution to set up an account with and start using. When you sign up for Paychex Flex Select, here is the experience you can expect to set up your account and run payroll:

    Set Up

    Paychex aims to have your new payroll system set up within 48 hours of you signing up. During the onboarding process you’ll receive one-on-one phone support from a Paychex implementation specialist. Simply provide them with your business and employee information, including your business’s tax ID number and your employees’ bank account information, and they’ll take care of the rest. If you’re migrating over from another payroll system, the implementation specialist will help you pull data and even process your first few payrolls after setup to show you how it’s done.

    Once you’re onboarded, your implementation specialist becomes the dedicated account manager for your business and is your point of contact going forward for any inquiries regarding your service.

    Running Payroll

    With Flex Select you have two options when it comes to running payroll: calling in your hours to your account manager or processing them online via your Paychex account or mobile app. If you decide to go with the latter option, Paychex tries to make the process as painless as possible.

    For starters, your account will notify you either via email or a message on your dashboard when your next payroll period is approaching. To run payroll, select the “Begin” option under “Current Payroll.” You’ll see a grid-like display of all your employees and the payroll information you entered for them during onboarding (salary, deductions, tax details, payment preference), including information for contractors and other part-time workers. Simply fill in the empty boxes on the grid for each employee’s hours worked, bonuses due, and PTO and sick time taken.

    Paychex will perform all the necessary calculations and determine what each employee is owed. If all looks right, you can request for payroll to be processed. Paychex places a 15-minute hold on all payrolls in case of last-minute adjustments and then distributes payment to your employees in accordance with their payment preferences.

    About those payment preferences, Flex Select offers a few options: direct deposit, paper check, or prepaid Mastercard. For businesses where employees get paid via tip, Flex Select provides a tip network function that allows you to pool tip amounts from all employees and distribute them electronically to an employee’s bank account at the end of their shift.

    Finally, Flex Select allows you to work ahead on payroll. If, for example, you don’t want to forget to give your employees holiday bonuses, you can adjust payroll for December months in advance.

    Paychex Alternatives

    With all of this information in mind, you may still be unsure if Paychex is right for you—or you may just want to compare it to some other options on the market. Here are some alternatives to consider:

    Automatic Data Processing (ADP)

    Another extremely popular payroll service provider is ADP (600,000 payroll clients). With ADP, you’ll get a lot of the same features you get with Flex Select, including new hire reporting, tax administration, and workforce reporting. But ADP offers four different payroll plans for small businesses, whereas Paychex offers four payroll plans total. ADP also integrates with more applications and offers time tracking tools with all its plans.

    Read our full comparison review of Paychex vs. ADP.

    Get Started With ADP Payroll


    You may also want to explore Gusto for your payroll needs. This cloud-based solution serves small businesses specifically and was first launched as a payroll-only service, so you can be sure their payroll features are top-notch. Beyond payroll, they also offer HR and employee management tools, and their three service plans are transparently priced (monthly base costs range from $39 to $149, plus per-employee fees). If you opt for their Concierge plan, you’ll also receive a dedicated HR professional, which can be especially helpful for small businesses that don’t have a dedicated HR department.

    For more information, read our Gusto vs. Paychex review.

    Get Started With Gusto Payroll

    PrimePay Payroll

    Unlike Paychex, PrimePay is designed specifically for small businesses. They feature transparent pricing ranging from $42 to $163 per pay period plus a per-check fee—and include all of their features with all plans. Those features include tax administration, new hire reporting, onboarding services, applicant tracking, and an HR advisory (for an additional fee).

    The Bottom Line

    We can’t deny that Paychex really does offer everything a small business owner could need in a payroll service. However, with so many payroll services out there, you’ll want to do your due diligence before making your final decision.

    Because Paychex pricing is quote-based, we recommend speaking to a Paychex rep to find out how much it will cost your business. Then shop around and see if anyone can match their services at a similar or lower price point. That way, you have a reliable service in Paychex to fall back on, plus other options to experiment with.

    Request a Free Quote From Paychex