Paychex Flex Review: Is It the Right Payroll Software for Your Business?

Paychex Flex is a cloud-based platform designed to help small businesses to enterprises manage payroll, benefits, and HR processes. It is an ideal payroll software for companies in a rapid growth phase, as it is easily scalable with flexible plans that can handle your growing HR and pay processing needs. It even offers mobile apps (for iOS and Android devices) that let you access payroll and HR tools while on the go.

Monthly fees start at $39 plus $5 per employee, and if you sign up for a Paychex Flex plan, you get three months of free payroll (as of this writing). In our evaluation of the best payroll software for small business users, Paychex earned an overall score of 4.33 out of 5.

Paychex Flex

Overall Score: 4.33 / 5

RATING CRITERIA	Pricing		3.00 / 5
	Payroll Features		4.13 / 5
	HR Features		5.00 / 5
	Reporting		5.00 / 5
	Ease of Use		4.50 / 5
	Expert Review		5.00 / 5
	Popularity		5.00 / 5

What We Like

• Flexible plans with a reasonably priced starter tier
• Multiple employee payment options that include paychecks with check signing services
• Has 24/7 support; offers a dedicated payroll specialist to its clients

What's Missing

• Pricing isn’t all transparent
• Year-end W-2/1099 tax reports, workers’ compensation, employee benefits, and time tracking are paid add-ons
• Access to a dedicated payroll specialist is available only in higher plans

Deciding Factors

• Ease of Use:
  • Software is relatively easy to learn and use, provided you have basic knowledge of how to run payroll
• Pricing:
  • Has three small business payroll plans—Essentials, Select, and Pro
  • Its starter Essentials tier costs $39 plus $5 per employee monthly; the other plans are custom-priced
• Software setup:
  • Paychex Flex is a cloud-based solution; doesn’t require manual software downloads
  • You can easily sign up for a Paychex Flex account via its website
  • Its online wizard will guide you through the setup process; those on the Pro plan get guided setup assistance
• Customer support:
  • 24/7 support via phone, email, and chat
  • Pro subscribers get a dedicated payroll specialist who can answer all of your pay-related questions

Visit Paychex Flex

What We Recommend Paychex Flex For

We’ve reviewed and compared hundreds of HR and payroll solutions, and Paychex Flex is one of our most highly rated—a top payroll service for businesses of all sizes. It offers solutions for onboarding new hires, paying employees and contractors, administering benefits, and managing online training programs to help boost employee development. Paychex even provides professional employer organization (PEO) services for companies that need expert assistance handling day-to-day HR processes.

In short, Paychex Flex is best for:

• Startups planning to grow significantly: Paychex Flex has multiple plans and features designed to grow with your business. Solopreneurs can start with Paychex Solo, and once their operations grow, they can sign up for Paychex Flex’s starter plan that comes with full-service payroll, new hire reporting, and payroll tax administration. If their business continues to expand, Paychex Flex has higher tiers they can transition to that include more HR tools and support like new hire onboarding, background screening, learning management, and access to a dedicated payroll specialist.
• Businesses with employees in multiple states: Paychex Flex supports payroll and tax processing plus compliance in multiple locations. It also offers health insurance and other benefits in all 50 states.
• Retailers and restaurants paying hourly workers: Paychex ranked high on our list of best restaurant payroll software because its system is robust enough to handle the payroll needs of restaurants (such as tip reporting and multiple pay rates) and even retail businesses. And if you get its time and attendance add-on, you can track the time of hourly workers and use its data to pay employees.
• Companies prone to workplace injuries and layoffs: Managing workers’ compensation can be a nightmare for many small businesses, especially construction and manufacturing companies. Paychex Flex offers a variety of insurance plans, one of which is workers’ compensation (although this costs extra). It also has state unemployment insurance (SUI) services that include constant monitoring of SUI regulations—provided you subscribe to its highest tier.
• Businesses needing PEO services: Paychex PEO, which is included in our best PEO companies list, takes away the burden of managing HR and payroll tasks yourself as it will handle these for you. It also utilizes Paychex Flex to manage employee benefits, new hire onboarding, and other HR processes.

When Paychex Flex Would Not Be a Good Fit

• Businesses with only 1099 contract workers: Although many industry experts say independent contractor growth is outpacing employee hiring, Paychex Flex does not yet offer a more affordable contractor-only payroll package. If you’re primarily paying contractors, consider either Gusto or Square Payroll, as both have low-cost contractor-only plans ($6 and $5 per contractor monthly, respectively). For other options, check out our top picks for contractor payroll services.
• Companies looking for an all-in-one HR software: Paychex Flex’s HR solution suite may be more robust than many payroll providers offer but it lacks a few advanced HR tools, such as compensation planning and employee performance reviews. If these features are critical to your business, consider either TriNet Zenefits or Paycor, as both have a wide range of HR solutions that even include staff surveys to help you monitor and improve employee engagement.

Top Paychex Flex Alternatives

Visit Gusto	Visit QuickBooks Payroll	Visit Square Payroll
Best for: Small companies needing payroll and basic HR	Best for: QuickBooks accounting small business users	Best for: Retailers, restaurant owners, and Square POS users
Base monthly fee from: $40 plus $6 per employee	Base monthly fee from: $45 plus $5 per employee	Base monthly fee from: $55 plus $5 per employee
Read our Gusto Review	Read our QuickBooks Payroll Review	Read our Square Payroll Review

In our evaluation of Paychex Flex’s pricing, this provider only earned a 3 out of 5. It lost points mainly because it doesn’t offer unlimited pay runs and not all of its plans have transparent pricing.

With Paychex Flex, you get three plans: Essentials, Select, and Pro. The Essentials plan costs $39 plus $5 per employee, while the other tiers require you to contact Paychex and request a quote. The main difference between the three is access to a dedicated payroll specialist and advanced HR tools and support, such as onboarding, learning management, SUI services, and guided setup for new clients.

*Additional fees may apply

Paychex Flex also offers these services at no extra cost:

• Paycard payment option: Electronically deposit salary payouts to prepaid cards
• Financial wellness program: Tools and educational courses to help employees meet financial goals
• Tax credit services: Expert assistance in finding and applying tax credits your business may qualify for
• Employee assistance program (EAP): Helps employees find solutions to personal issues that may affect their work productivity

Apart from these services, Paychex has add-on solutions like time tracking tools and employee benefits (such as retirement, dental, vision, and health insurance plans). However, these solutions are custom-priced—you have to contact Paychex to discuss your requirements and request a quote.

Paychex Flex didn’t get a perfect score in this criterion, earning only a 4.13 out of 5 for pay processing. The additional fees for year-end W-2/1099 tax reports and its tax penalty guarantee that only covers mistakes that Paychex’s representatives make cost it some points.

Despite some of the limitations of its payroll tax services, its online pay processing tools are designed to help you accurately pay employees and contractors on time. Not only does it have all the tools you need to calculate earnings and deductions but it provides compliance support so you can manage tax regulations, workers’ compensation claims, and unemployment reporting with ease.

Paychex Flex’s Payroll Center shows your current and future pay periods, allowing you to easily start and resume pay runs. (Source: Paychex)

Pay Processing

Online payroll processing is the main feature of Paychex Flex. It can handle pay processing for hourly and salaried employees, including contract workers. Aside from direct deposits, it supports employee payments via pay cards and paychecks. However, paychecks with signing services are available only in its higher tiers.

Wage garnishments are deducted automatically and remitted to the appropriate agencies. You can customize earnings and deductions, and its system will calculate the applicable amounts. Paychex Flex even lets you choose from several pay entry options, including a grid view for easy data entries while running payroll.

Paychex Flex’s customizable pay entry option lets you select the layout, data filters, and how pay items and employee information are organized.
(Source: Paychex)

Payroll Taxes

Payroll Mobile App

Paychex Flex makes running payroll easy with its mobile app (for iOS and Android devices). Rated as one of our best payroll apps for small businesses, it lets you resume pay processing that you started on your computer and submit payroll directly from your smartphone or tablet—provided internet connection is available.

Aside from running payroll, Paychex Flex’s mobile app allows you to access PDF versions of basic payroll-related reports. (Source: Paychex)

Paychex Voice Assist

Paychex Flex earned perfect marks in this criterion given its solid HR tools for managing new hire reporting, onboarding, and employee benefits. The coverage of its health benefits is also excellent as it is available in all 50 states, unlike that of other payroll providers (like Gusto, which is limited to 39 states). Plus, you’re granted access to Paychex’s other HR services and solutions (although some cost extra) like learning management, time tracking, and a library of HR documents and business forms that you and your employees can use.

Employee Benefits

Time Tracking

Paychex Flex Time, which is available as a paid add-on, captures employee clock-ins/outs, manages staff schedules, and tracks paid time off (PTO). Its biometric and facial verification time collection methods prevent buddy punching and time theft.

It also has a mobile app, Paychex Time, through which employees can clock in/out, switch jobs or assignments, and request PTO. For those tracking the hours worked by field staff, its geolocation feature can help you check the location of employees who are clocking in, while its geofencing capabilities allow you to set up virtual perimeters around designated areas where your staff are allowed to punch in.

With Paychex Flex Time, employees can send time cards and time-related pay adjustment requests to their manager for approval. (Source: Paychex)

HR Tools

Paychex Flex’s HR solutions include a digital library of HR and business forms that you can use. If you need to run background checks on qualified candidates who meet your hiring requirements, the Paychex Flex Pro plan comes with a limited number of background screens. In addition to new hire reporting, you get onboarding tools that enable your new hires to complete required documentation online, such as direct deposit and tax forms.

Its platform also lets you store documents like company policies and forms. And if you subscribe to Paychex Flex’s highest tier, you get an online employee handbook builder with options to create Microsoft Word or PDF file documents for easy distribution.

Your new hires can access documents, forms, and policies that they need to fill out or review from within Paychex Flex’s onboarding tool. (Source: Paychex)

Learning Management

PEO Services

This is another criterion where Paychex Flex earned a 5 out of 5 rating. Its robust reporting tool provides you with more than 160 standard reports and analytics—payroll journals, employee turnover rates, headcount reports, labor cost summaries, and more. Aside from letting you create custom reports, it has data visualization capabilities so you can view the information in various graphs and pie charts.

You can customize your Paychex Flex dashboard to show data and analytics that are important to your business.
(Source: Paychex)

• Data migration services for new clients are available
• 24/7 customer support with US-based specialists
• Phone, chat, and email support
• Access to a dedicated payroll specialist
• Library of HR forms and business documents
• How-to guides and help articles

Paychex Flex received high ratings (4.5 out of 5) in ease of use because of its intuitive platform. Its online tools are relatively simple, but learning to navigate through all of its features may take some time.

While it provides guided onboarding and setup to new clients, this is available only in higher tiers. However, signing up for a Paychex Flex account online and adding your employee and company information is fairly straightforward—provided you have all the data available and only a handful of employees.

Those on the Paychex Flex Select and Pro subscriptions are also granted access to a dedicated payroll support specialist. This means you can contact a payroll expert who knows about your business’ pay processing needs and can answer your phone and email queries in a timely manner. If you’re on its starter tier and have questions about its features, you can either access its how-to guides or contact Paychex’s 24/7 support (via phone, chat, and email).

In addition to setup assistance and 24/7 customer support, Paychex Flex offers application programming interface (API) integrations with various third-party software. It works with accounting, HR, banking, insurance, retirement, and time clock systems. Here are some of its partner solutions:

• Hiring and HR: Glassdoor, Indeed, SimplyHired, BambooHR, HireRight, and TalentReef
• Time and attendance: Deputy, OnShift, TIMECO, and QuickBooks Time
• Retirement and health benefits: Aetna, AIG, Ameritas, Cigna, Charles Schwab, Fidelity, Merrill Lynch, and Vanguard
• Finance and accounting: QuickBooks Online, Sage Intacct, SAP, and Xero
• POS: Clover
• Banking institutions: Chase, Capital Bank, Bank of America, and US Bank

Paychex Flex received perfect marks in this category given its solid payroll tools, efficient HR services, and reasonably priced starter plan. Startups and small businesses with plans to scale can rely on its feature-rich platform and wide range of HR solutions to handle their growing employee management needs. Paychex can even provide PEO services should you need HR professionals to help you run day-to-day HR tasks while ensuring compliance to federal and labor regulations.

This provider scored perfect marks in our popularity criterion because many Paychex Flex reviews on third-party sites are positive. It received 4 and up user ratings on G2 and Capterra, as well as a high number of average user reviews online (more than 1,000).

Reviewers said that Paychex Flex is generally easy to use and simple to set up. They added that its system is intuitive on the employee side and convenient to access due to it being hosted online. A few others appreciate that they have access to a variety of HR tools (like learning programs and time tracking) and a dedicated payroll specialist who can answer all their payroll and tax queries.

However, some users reported they had difficulties connecting with a customer service representative to help them with specific problems such as tax issues. One user shared that he dislikes connecting with separate support teams, depending on the Paychex Flex module (such as payroll, benefits, or time tracking) he has problems with.

At the time of publication, Paychex Flex reviews earned the following scores on popular user review sites:

• G2: 4.2 out of 5 based on nearly 1,400 reviews
• Capterra: 4.1 out of 5 based on about 1,300 reviews

How We Evaluated Paychex Flex

When we evaluate payroll software for small businesses, we look at pricing and ease of use. We also check the provider’s customer support and whether it offers unlimited pay runs, multiple pay options, full-service payroll, and tax filing services.

Access to third-party integrations and basic HR tools like employee benefits and onboarding are also important. We even consider the feedback that actual users posted on popular user review sites.

Click through the tabs below for a more detailed breakdown of our evaluation criteria:

Bottom Line

Whether you’re a solopreneur or a small business planning to expand to a midsize or large operation soon, Paychex Flex can grow with you. With over 45 years of providing HR and payroll solutions and services, it has the experience and resources to help your company scale. It has a wide range of HR solutions for managing the entire employee lifecycle, from hiring to retiring. Sign up for a Paychex Flex plan today.

Visit Paychex Flex

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