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

Paychex Flex helps small to enterprise-sized businesses manage their payroll online via its mobile app. It is an ideal payroll solution for businesses in a rapid growth phase, as it is easily scalable and includes onboarding support and new hire reporting.

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What We Recommend Paychex Flex For

After testing and reviewing hundreds of HR, payroll, and accounting SaaS solutions over the years, I can easily report that Paychex has done one thing right: It is simple to use, as the interface is not crowded with extra features. It only takes only a few minutes to set up if you start using the small business basic product, Paychex Go. It will take two days if moving data from another provider. It took me about five minutes to set up a new business account.

In short, Paychex Flex is best for:

• Startups planning to grow significantly: Paychex Flex offers on-boarding and new hire HR support, helps train your new employees to use the system, and provides new hire reporting options. If you’re using its basic Paychex Go product, you can add employees for only $4 each per month. It also has three higher tier plans you can transition to when if you grow and need more personalized service in addition to HR support.
• Retailers and restaurants paying hourly workers: The payroll system tracks time worked and attendance. It can also support numerous payment options. It monitors breaks, shift swapping, and overtime alerts and supports time card approvals if needed.
• Manufacturing companies prone to workplace injuries and layoffs: Managing workers’ compensation can be a nightmare for many small business owners, especially construction and manufacturing companies. Paychex Flex offers a variety of insurance plans, and it includes an integrated Workers’ Compensation Payment Service. It also offers a state unemployment insurance (SUI) add-on that includes constant monitoring of SUI regulations.
• 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.

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 contract-only package. If you’re primarily paying contractors, check out our top picks for contractor payroll services.
• Small businesses not planning on growth in the immediate future: The entry-level product doesn’t include features such as the mobile app, business software integrations, unemployment services, customized reporting, and on-boarding tools; when you’re just starting out, your goal is usually to get the most bang for your buck. If you have a small operation, check out our guide on payroll software for small businesses to find a better fit.

Paychex Flex Overview

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Paychex Flex Pricing & Features

Setting up this payroll service is simple. I was able to set up a basic Paychex Flex Go account in less than five minutes. If you have many employees to add with different payment types, it will take longer, of course. Paychex Flex can help you set up your account or migrate data if needed. The software runs checks, too, so you don’t miss anything when setting up payroll processing.

You can sign up for a Paychex Flex Go account easily online on your own. If you need a Select, Pro, or Enterprise account, you’ll need to contact a customer service representative to help you build your customized plan.

Payroll Processing

Online payroll processing is the main feature of Paychex Flex. It can process various types of payroll processes, including managing hourly, salary, and contract hours. It can also support direct-deposit payments, as well as payment cards and checks.

It is easy to select a payroll schedule using Paychex Flex. You can choose weekly, biweekly (every two weeks), and monthly or create a customized pay period.

Payroll Taxes

Paychex Flex can manage employee federal, state, and local payroll taxes for every state. To help you file accurate taxes, it employs hundreds of people dedicated to monitoring tax law changes. They calculate, pay, and file your payroll taxes for you. Paychex Flex will also help you find tax credits that your business may qualify for.

Paychex Flex supports full-time, part-time, and 1099 contract workers.

Time Tracking

To create accurate payments, the software tracks time, including breaks and overtime. You can set it up to require payment approvals if necessary. You can use it with Paychex Flex Time or a third-party time tracking solution, including those that support hand, iris, and face scanning.

Business Software Integration

Payroll software is nearly useless if it does not integrate with your other business solutions. Paychex Flex works with accounting, HR, time clock, banking, insurance, and retirement systems. It says it works with POS software, too, but we found that it is only compatible with Clover. However, with regard to retirement and health services, it works with many, including popular services such as Aetna, AIG, Ameritas, Cigna, Charles Schwab, Fidelity, Merrill Lynch, and Vanguard.

It is also compatible with  popular accounting software, HR, point-of-sale (POS), and productivity solutions,

• QuickBooks
• Sage
• Xero
• Indeed
• Bamboo HR
• Clover
• SAP

And of course, it offers integrations for working with most major banks, such as Chase, Capital Bank, Bank of America, and US Bank.

You can set up a variety of payroll deduction types. The Pro and Enterprise version supports more options than the Flex Select and Flex Go versions.

Payroll Support

Paychex Flex Select, Pro, and Enterprise versions provide a dedicated payroll support specialist. This means you can contact a specialist who knows about your business and answer their phone and email queries in a timely manner. This support person is U.S.-based, or if you’d rather visit an office, Paychex Flex supports over 100 office locations across the U.S.

Employee Training

While the software is simple to use, Paychex Flex offers employee training support to larger companies, including online courses, an AI-powered learning management system, and printable training posters. New-hire onboarding tools include direct deposit and tax forms that can be processed using paper or paperless using the mobile app.

Paychex Professional Employer Organization (PEO) Services

If you want to outsource your business’ key HR functions, then you may want to consider Paychex’s PEO services. Ideal for growing companies with at least five employees and limited HR support, it comes with a comprehensive range of HR services—most notably its large group benefit rates and HR experts help you stay compliant with laws and regulations

Paychex PEO HR Experts

These professionals can deliver personalized recommendations and advice, depending on your business’ objectives, risk tolerance, and needs. They can also assist in updating your company policies, including creating and managing a company culture strategy to boost employee engagement. If you’re regulated by OSHA (such as companies that do manufacturing or deal with chemicals), you’ll find having a dedicated safety representative handy. This service will help you handle OSHA regulations and manage your workers’ compensation insurance.

Paychex PEO Benefits & Insurance

With Paychex PEO, you get access to employee benefits programs like health insurance, dental, vision, 401(k) plans, and health benefits accounts (such as FSA, dependent care FSA, HSA, HRA). Paychex will also assist you in managing these benefits through Paychex Flex, so deductions and premium contributions flow smoothly. Employment practices liability insurance (EPLI), cyber liability insurance, and state unemployment insurance (SUI) administration are also available.

Paychex PEO Pricing

Pricing varies depending on your location and number of employees. Paychex PEO charges a flat rate per employee vs a percentage of payroll, which can be more affordable if you have high-salaried employees on staff.

Paychex Flex Ease of Use

Top Paychex Flex Alternatives

What Users Think About Paychex Flex

Most small business owners gave Paychex Flex positive reviews with an average score of 4.2 out of 5 stars. Customers reported that the software is easy to use, simple to set up, intuitive on the employee side, and convenient due to it being hosted online. The mobile app also received positive remarks. However, some reported that they had difficulties connecting with a customer service representative to help them with specific problems such as tax issues.

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

• Software Advice: 4.07 out of 5 based on 1,003 reviews.
• G2: 4.5 out of 5 based on 1,185 reviews.
• Capterra: 4.1 out of 5 based on 1,003 reviews.

When reading through user reviews, here are some of the trends that I noticed:

Bottom Line

If you are planning to expand to a midsize or large operation soon, Paychex Flex can grow with you. It is a large established company, reporting to pay one in every 12 American private-sector employees, that has the experience and resources to help your company scale. If you will need HR support alongside the payroll solution, Paychex Flex has over 600 HR professionals on staff to help you. Plus, your HR and accounting teams will appreciate how easy the payroll service is to use. Sign up for a free Paychex Flex demo today.

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