Paychex Flex HR Software Review 2025

Why Paychex Flex Is the Best HR Software for Remote Teams

Of the HR software providers we reviewed, Paychex Flex offered some of the most remote-friendly features. These features include 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 helpful for employers who must juggle compliance requirements across different cities and states.

The platform also offers excellent employee self-service tools on both the web platform and the mobile app. We got to test some of these self-service tools in the Paychex interactive product tour and were pleased with how easy they were to use. Remote employees don’t have the benefit of hands-on, in-person support to walk them through new HR systems or processes. For that reason, remote employees will need access to user-friendly tools and self-service platform training resources. Paycheck Flex made this simple to do. We also found its tutorial content very easy to follow when we were learning how to use these tools proficiently.

We also appreciated the new Paychex Flex predictive analytics features that draw on data and trends. These features help you plan for retention and turnover, diversity, compensation and hiring. On the employee side, a new interactive calculator and goal tracker also helps workers stay on track with their retirement planning goals.

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

Usability

Paychex offers a relatively simple user interface. If you’re transitioning from a spreadsheet or an accounting-oriented provider, such as QuickBooks, you may feel right at home with its classic look and feel. But if you’re used to newer solutions, like the ones in our TriNet review and Rippling review, Paychex may feel slightly outdated. 

That said, we like that the Paychex dashboard provides a clear overview, giving you instant access to your current and most recent payroll. It also provides 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.

Paychex users have the option to run payroll from any computer or hand-held 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 nationwide relying on a fully or partially remote workforce, accessing information and accomplishing tasks from anywhere makes Paychex an attractive service.

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)

Employees can use Touch ID and/or Face ID to access their pay stubs, W-2s, 401(k) plans, balances and health-related benefits from the mobile app. Administrators can also access a variety of features in the mobile app, including payroll processing tools and HR reporting. Administrators can view reports of labor costs, turnover and current hiring metrics conveniently from their smartphone. We found this feature superior to those of some competitors, whose reporting tools were not as mobile-friendly.

Paychex Flex Features

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 help manage 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 can pay employees via direct bank deposit or deposit to a pay card, and it can also allow employers to print checks.  In addition, users can access more than 160 standard payroll reports or customize their own reports and data visualizations.

Use the standard or customizable reports in the Paychex Flex platform to view payroll information with helpful data visualizations. 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 with employees spread across many regions. Paychex calculates, files and pays all of your payroll taxes on your behalf. Additionally, the company can file all of your W-2 or 1099 forms accurately and on time. If there are mistakes, Paychex takes care of any tax penalties you may incur.

Integrations

The Flex Select and Flex Enterprise plans offer the ability to link your company’s payroll data to many accounting software programs securely, 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 offers more integration options than several of the competing HR software vendors we reviewed.

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

Onboarding

You can eliminate physical 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. 

On the employee end, the onboarding process is clear and relatively efficient. Remote employees benefit from the paperless experience, eliminating the need for printing or scanning. Employees can even access and fill out their onboarding materials from a smartphone. Paychex Flex has also recently incorporated a new survey into the employee onboarding process to determine whether your company is eligible for a Work Opportunity Tax Credit (WOTC).

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. They can also guide you through Occupational Safety and Health Administration regulations, state unemployment insurance administration, payroll processing and health benefits enrollment. Businesses can utilize this add-on service to consolidate their buying power for benefits normally available only to much larger organizations.

Hiring

Paychex’s optional hiring integration helps companies recruit, screen and hire applicants from one simple dashboard. Paychex also integrates with a variety of job sites, applicant tracking systems and other hiring tools. 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 candidates’ qualifications, reducing employee turnover, and minimizing potential claims of poor or illegal hiring practices.

Paychex PEO 

Paychex provides flexible, scalable PEO services that combine the user-friendly Paychex Flex tech platform with hands-on support and guidance from HR experts. Under the PEO service, Paychex acts as a co-employer alongside your business. Paychex PEO includes personalized payroll, benefits and onboarding support from Paychex’s HR experts and mobile-friendly cloud-based HR software tools. Paychex’s seamless digital onboarding experience makes them an excellent option for employers onboarding remote team members or simply looking to provide a more seamless onboarding experience.

Paychex PEO Pricing

Paychex provides a bundled package of PEO services, and you can mix and match additional services to customize your own PEO solution. This is a major advantage for startups and growing companies that don’t want to pay for services they will not use. Paychex PEO customers also have access to a dedicated point-of-client HR professional to provide proactive advice. From payroll and benefits to recruitment and safety, customers also have access to other experts on various topics.

Onboarding

Having a strong onboarding experience is the key to making a positive first impression with new hires. Paychex recently revamped its employee onboarding tools to deliver a more seamless onboarding experience. New hires receive an invitation to the platform and can then access a well-organized onboarding list. From there, new hires may complete paperwork and set up their payroll information, including selecting their withholdings and enrolling in direct deposit. Employees can go through all their onboarding paperwork from a mobile device. Onboarding tasks can also be tracked on the Paychex platform dashboard.

Benefits

Under the PEO model, Paychex administers benefits to employees. Employees are eligible to enroll in health benefits under Paychex’s selection of group health plans and other benefits. This is a great way for small businesses to offer stronger benefits to their employees. Like with onboarding, the benefits enrollment process can be completed on desktop or mobile through a simple online workflow. 

HR Administration

Paychex can manage all of your administrative HR tasks, such as creating an employee handbook and policies and writing job descriptions. It can also manage recruiting and onboarding employees, handling new-hire reporting, processing payroll, and assisting you with employee termination. We found the employee handbook and policy tools particularly helpful for startups. Having an employee handbook is important, but handbooks can be challenging and time-consuming for startups to create.

Employee Training and Development

Paychex provides one of the best training programs of any PEO we reviewed. It offers online books, videos and courses on a range of topics. Topics include professional development, soft skills, computer and technical skills, HR, workplace safety and conflict management. This is a great resource for small businesses without internal training resources.

Paychex HRO

When partnering with Paychex for human resources outsourcing, businesses can access comprehensive HR services, including risk management, payroll, employee benefits, HR administration, and training materials and courses. Additionally, customers gain access to a dedicated HR professional who can serve as an advisor to the business throughout its partnership with Paychex. Paychex HRO customers also receive access to Paychex’s all-in-one HR tech platform, Paychex Flex.

Paychex HRO Pricing

Because Paychex’s HRO plan is available to businesses of all sizes, even those with just one employee, it offers a lot of flexibility. There are no minimum salary requirements or required contract lengths. You can cancel at any time by providing 30 days’ notice. Paychex is great for small businesses with unique HRO needs, as it offers a variety of features packaged into different HRO options. The plans are scalable, so you can add services or products as your business grows. Like many other HRO services, Paychex does not openly advertise its pricing

Payroll

Paychex is one of the best in the industry at running payroll and offering insightful reporting. It is well designed for small companies, which often have only one person dedicated to managing payroll. Paychex customers can use the payroll processing software to track employee hours, including paid time off and sick days. The payroll service also includes compliance with government regulations, state and local tax preparation, time clock technology and other key payroll features. Paychex also provides a well-tested mobile app for payroll and HR management on the go. 

Paychex’s payroll services and tools are very well-regarded in customer reviews. When we tested the platform ourselves, we were equally impressed by how user-friendly the payroll processing tools were. Additionally, we found the in-depth payroll reporting features to be particularly useful. Paychex also offers some flexible payroll options that others don’t, such as off-cycle payments, contractor payments and direct deposit to prepaid debit cards.

Employee Benefits

Through the HRO model, Paychex offers guidance on benefits support and related needs. The company provides advice and can guide you in selecting a third-party benefits provider that suits your workforce needs. You and your employees can manage your benefits online through the Paychex platform, even though these benefits are provided by a third party. Paychex also helps you find the right benefits plan for your business and educates you on the various health insurance options available to your team. This differs from the PEO model, where Paychex directly offers benefits to eligible employees.

Risk and Compliance

Remaining compliant with state and federal regulations is critical for any business. Failure to do so could result in fines and lawsuits. Depending on the severity of the fines or lawsuits, falling outside of compliance can even lead to permanent business closure. To help you avoid these pitfalls, Paychex makes sure your business complies with all existing HR regulations and all legal requirements. This includes considerations like COBRA, required annual reporting, workplace safety training, development of workplace safety policy and guidelines, workers’ compensation, return-to-work programs, unemployment insurance, and on-site safety inspections. Paychex Flex has 200-plus experts monitoring changes in laws and regulations that could affect your compliance. Plus, the platform offers a convenient HR Library to help businesses stay up to date on the latest laws and standards.

Paychex Flex offers an HR Library with a state comparison tool that allows businesses to keep up to date on the latest regulations and stay in compliance. Credit: Paychex Flex

Paychex Costs

Paychex offers three subscription options designed to fit the needs of small, midsize or enterprise-level businesses. The entry-level pricing for the Paychex Flex Essentials plan starts at $39 per month plus $5 per person. We were pleased to see the transparent pricing. However, prospective customers should note the Essentials plan is geared for companies with one to 19 employees. For the Flex Select and Flex Enterprise plans, you will need to contact Paychex to get a quote.

Add-ons for job posting website integrations, time tracking and attendance, performance management, job costing and labor forecasting, retirement services, business insurance and employee benefits 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, employee onboarding, standard analysis and reporting, direct deposit and/or pay cards, employee self-service and mobile experience, financial wellness and cash flow assistance, automatic W-2s and 1099s, and U.S.-based customer service.

Paychex Flex Select

• Pricing: By custom quote only
• Standout features: A learning management system, integrations with many third-party tools, HR Library access, labor posters, online payroll and tax filing for businesses of all sizes, and 24/7 support from dedicated specialists. 

Paychex Flex Enterprise

• Pricing: By custom quote only
• Standout features: Robust HR software and handbook tools with a personal consultation, full-service setup, general ledger service, garnishment payment service, preemployment screening, workers’ compensation reports and payment services, and state unemployment insurance services.

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.

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

Paychex Flex Time and Attendance

Paychex offers two timekeeping plans for small businesses looking for the best time and attendance tools, which can be purchased separately or added to the Paychex Flex platform. The solutions fully integrate with Paychex Flex and have several time clock options. We were impressed with both plans’ employee self-service features and geotracking capabilities. This is especially true since some competitors lock these tools behind more costly plan tiers.

Paychex Flex Time and Attendance Pricing

As noted with other Paychex Flex subscriptions, Paychex doesn’t provide pricing information for all plans online. You must contact the company for a custom quote. However, the information provided by a Paychex representative showed the costs are in line with other time and attendance solutions like When I Work and QuickBooks Time. The price drops further if you bundle the time and attendance solutions with other Paychex tools. 

Here are the three time and attendance service plans, with pricing provided for 22 or 23 employees:

• Paychex Flex Time Essentials: For $59 per month, or roughly $2.57 per user, Paychex provides self-service tools and online timesheets, and time clock options, including web based, mobile and a kiosk app with facial verification. The plan offers timecard approval functionality, a visual scheduler, overtime rules, job costing and geofencing.
• Paychex Flex Time: For $99 per month, or about $4.30 per user, Paychex offers additional time clock methods like biometric iris and finger scan and interactive voice response (IVR). On top of all the features from the Essentials plan, this plan adds shift swapping, schedule templates, additional alerts (like approaching overtime notices) and messaging tools, leave management, mileage tracker, and real-time analytics.
• Time-off Management: For $29 per month, or roughly $1.26 per user, Paychex gives salaried workers self-service tools for basic timesheet management as well as leave accrual, tracking and request features. The time-off management product can be set up as a stand-alone feature with Paychex Flex, or used in combination with the full-featured Paychex Flex Time.

Time Tracking

Paychex provides Android and iOS mobile apps for clocking in and out, regardless of the subscription. But the system also offers web-based time clocks and a kiosk app you can use with your own tablet. Like TimeClock Plus, Paychex has physical time clocks, including a contact-free iris scanner. Alternatively, users can call in using an IVR service.

Administrators and managers can view employee statuses, including who is logged in or on break, through the dashboard. It also alerts business leaders to potential issues, like an absent employee or missing timesheet.

Employee Scheduling

Paychex’s scheduling capabilities let employers create templates and duplicate shifts, which is similar to competitor products. Employees can connect Paychex to their preferred online calendar and view scheduled shifts within that program. Or they can check their schedule on mobile apps or any time-clock device. We liked how workers can choose to receive scheduling alerts via email, text or smartphone notification. 

Leave Management

Along with time tracking, employees and supervisors can view and manage PTO accruals and time-off requests from a smartphone, computer or time clock device. On the administrator dashboard, leaders can view all pending and approved requests on a calendar and see a list of all pending requests requiring action. We appreciate the ability to block out dates, which can help companies during peak seasons.

Geotechnology

Not all time and attendance tools offer GPS tracking and geofencing. But Paychex builds these capabilities into both time tracking plans. When enabled, all mobile logins show a pin icon, and employers can click it to see where the employee clocked in based on GPS or geofencing data. Paychex also uses geotechnology to automatically record mileage, making Paychex an excellent solution for expense tracking.

Time and Attendance Reporting 

Paychex provides on-demand reports and a real-time dashboard. Both solutions increase visibility into your labor costs and key performance indicators (KPIs). Employers can compare scheduled and actual hours between weeks and monitor timesheets for accuracy. With the ability to schedule reports, managers can see the metrics that matter most without repeating the same steps weekly. 

Paychex 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 information to set up your year-to-date payroll data, including your employee and business information. 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.

Then, an implementation specialist will set up your account. They will audit back to the beginning of the year and balance your year-to-date payroll data. They’ll also stay with you for your first few payroll cycles. You will be assigned a payroll specialist who will be your main contact going forward.

Paychex Flex Customer Service

Administrators and employees can reach a member of Paychex’s U.S.-based customer service team by phone, chat or an online form 24/7. Many competitors offer support only during an 8-to-10-hour window each day, so 24/7 support is a major perk. It’s particularly helpful for remote teams, as employees may be spread out across different time zones or may work more flexible schedules. With 24/7 support, your employees will always be able to reach someone during their work hours.

Flex Select and Flex Enterprise customers are assigned a highly trained payroll specialist who serves as the key point of contact for help with tax or payroll needs. This one-on-one dedicated support can be extremely helpful for employers managing remote teams, as it can be tricky to navigate the different payroll and tax requirements in each state where you have work-from-home staff. Paychex also maintains a self-guided library of useful how-to guides and tips to improve your HR department’s operations.

Paychex 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 costs of their services. For us, transparency gives more confidence when shopping and comparing service providers. 

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 salaried staff and hourly workers biweekly and run a one-time bonus for top salespeople, you’ll incur five payroll-related charges in one month. If you need to correct any errors along the way, those errors also count as additional payroll runs. 

We recommend 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. See our Gusto review and Paychex vs. Gusto comparison for an example of transparent pricing with unlimited payroll runs.

Methodology

We conducted comprehensive research and analyzed leading HR systems to identify the best HR software solutions on the market. We watched Paychex product videos and took the company’s interactive product tour. When looking for the best HR software for remote teams specifically, we prioritized features such as the ability to automate local payroll taxes and compliance, a paperless onboarding experience, and strong employee self-service features.

Overall Value

We recommend Paychex Flex 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 Flex for …

• Companies that value a more 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.