Paychex Flex vs. QuickBooks Online Payroll: Which Is Best for Your Business?

How Paychex Flex and QuickBooks Online Payroll compare and which payroll provider is best for your business.

Nina GodlewskiOct 28, 2020
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Paychex Flex and QuickBooks Online Payroll are both popular online payroll products for small-business owners. Paychex Flex stands out by offering a dedicated payroll specialist and a variety of payment options, while QuickBooks Online Payroll offers health benefits administration and, with its most expensive plan, tax penalty protection.

Paychex Payroll plans and pricing

Depending on your business needs, Paychex likely has a plan designed specifically for you. It has several plans for different business sizes and needs. Keep in mind that the pricing for each plan is quote-based.

Paychex Flex Select

The Paychex Flex Select plan is specifically designed for small businesses with fewer than 50 employees that need comprehensive payroll software.

The features included in the Paychex Flex Select plan are:

  • Payroll tax administration: All of your payroll taxes on a local, state and federal level will be filed and paid for on behalf of your business so you don’t need to worry about doing it yourself.

  • New-hire reporting: Your new hires and contractors will be taken care of when it comes to new hire reporting rules in your state.

  • Free mobile app: You’ll have access to the Paychex Flex app to access payroll on your phone so you’ll be able to run payroll from anywhere.

  • Customer support: Access support from specialists 24/7 via phone or chat.

  • Dedicated payroll specialist: With Paychex, you’ll be assigned a dedicated payroll specialist who you can contact with any questions you have about payroll or taxes.

  • Labor force poster kit: Paychex will send you state and federal worker information to display in the workplace to stay in compliance.

  • Employee financial wellness: Your employees will be able to access educational tools to help them make smart financial decisions.

  • Direct deposit and/or paycards: Pay your employees with direct deposit or with a prepaid paycard.

  • Employee and income verification services: This is an automated service that can confirm employment and income information on behalf of employees.

  • Additional employee pay options: In addition to direct deposit and paycards, you also have the option to pay employees via paper check or check signing.

Paychex Flex Pro

This Paychex payroll plan is best for businesses that have 50 employees or more. There are also some other features you’ll get in addition to everything included in the Select plan.

The additional features that come with the Flex Pro plan are:

  • General ledger service: You’ll be able to link your accounting software to Paychex if you use QuickBooks Online, Sage Intacct or Xero.

  • Workers compensation report: You’ll receive a report to review information about wages that are subject to workers compensation and premium information.

  • State unemployment insurance service: You’ll also get help with managing the unemployment insurance for your employees.

  • Analytics and reporting: Paychex can create more than 160 reports to help you get insights into your business.

  • Garnishment payment service: You can set up Paychex to automatically deduct garnished wages.

  • Paychex Flex onboarding essentials: Employees can complete their tax forms and direct deposit online when they’re starting and onboarding.

  • Paychex employee screening essentials: Get a limited number of background checks for your potential new hires.

Paychex Flex Enterprise

If your business has 100 employees or more, this is the Paychex plan you will need. You’ll get all of the features included in the Select and Pro plans, plus more.

The additional features include:

  • Custom analytics and reporting: Get reports and visualizations created especially for your business’s needs.

  • Paychex Flex HR administration: Create a structure for feedback and development with schedule creation and employee training, all stored in the cloud.

Paychex pricing

The pricing for all the Paychex payroll plans is quote-based, so it’s not exactly clear what to expect in terms of cost. This also makes it a bit more difficult to compare Paychex to QuickBooks Online Payroll. The lack of upfront pricing from Paychex can also be seen as a lack of transparency from the service.

QuickBooks Online Payroll plans and pricing

One of the biggest names in business software is QuickBooks (owned by Intuit), so you’ve likely come across them in some capacity already. There are three versions of its payroll software depending on the features you need for your business.

QuickBooks Payroll

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on QuickBooks's website

QuickBooks Core

The QuickBooks Payroll Core plan costs $45 per month and an additional $4 per employee per month. The features that come along with this plan are:

  • Unlimited payroll runs: View and approve payroll or run payroll automatically for salaried employees. Easily make changes for bonuses or extra compensation as necessary.

  • Next-day deposit: Submit payroll by 8 p.m. ET, and employees will get their deposit the next day.

  • Tax deductions: Taxes and other deductions from paychecks will be automatically made and adjusted for you as necessary.

  • Tax filing: State and federal taxes will be calculated and filed on your behalf at the end of the year.

  • Workforce portal: Allow employees to see their W-2s, their deductions and their PTO allowances online in the employee portal.

  • Payroll reports: Run reports around payroll, from history and bank transactions to PTO statistics and tax payments.

  • Health benefits administration: Manage your employees’ health benefits from the QuickBooks payroll portal.

QuickBooks Premium

If you opt to move up to the Premium plan, you’ll pay $75 per month and an additional $8 per employee per month.

In addition to the features in the Core plan, you’ll also get access to additional features:

  • Same-day direct deposit: Instead of having to wait a day, you’ll be able to run payroll and make the deposits in the same day.

  • HR support center: Get HR support from experts at Mammoth on state and federal overtime laws, hiring, firing and onboarding.

  • Workers comp administration: Get quotes from QuickBooks’ broker, AP Intego, to compare pricing and plans for workers comp.

  • Time tracking on the go: GPS allows you to track employees’ whereabouts and they can clock in and out from anywhere using the TSheets mobile app integration.

  • Expert setup: An expert will review your payroll setup to make sure you filled everything out correctly.

QuickBooks Elite

The highest-level plan, QuickBooks Elite, costs $125 per month and an additional $10 per employee per month. This plan includes all the features in the Premium and Core plans, plus even more.

The additional Elite plan features include:

  • Customized setup: A QuickBooks expert will set up your new payroll system for you so you can be sure it’s done correctly.

  • 24/7 expert product support: U.S.-based support experts will be available to you whenever you need technical support. They’ll even call you so you don’t need to wait on hold.

  • Time and project tracking: Track expenses and hours on the go so there’s no playing catch up.

  • Tax penalty protection: If there are any IRS penalties due to QuickBooks filing your payroll taxes, it’ll cover the cost up to $25,000 including interest each year. Its team will also represent you to resolve the issue.

  • Personal HR advisor: Work with a personal HR advisor from Mammoth by phone or online; they’ll also work with you to create custom handbooks and policies.

Paychex Flex advantages

Dedicated payroll specialist

No matter which Paychex payroll plan you choose to go with, you’ll get a dedicated payroll specialist. This can be incredibly helpful for small businesses, especially if you don’t have an HR specialist on staff. This is an advantage for Paychex because it is included with every plan it offers, while QuickBooks only offers it with its more expensive plans.

Your specialist with Paychex can help answer any questions you have around your payroll or taxes, which can help you avoid making any mistake that might end up costing you in the long run.

Variety of payment methods

Another area that sets Paychex apart is that you can pay your employees in a variety of ways. You have the option to pay them via direct deposit into their personal account or with a prepaid paycard.

If neither of those options works for you, you can also pay them via paper check. Along with those paper checks, you can get access to check signing and check logo service to personalize the checks for your business. While this isn’t something every business owner will need or use, it is key for those who do need it.

QuickBooks Online Payroll advantages

Tax penalty protection

The tax penalty protection only comes with QuickBook’s most expensive plan, but it might be well worth it if your payroll taxes are particularly complex. QuickBooks will cover you in the event that you receive a tax penalty from the IRS.

QuickBooks will pay all penalty fees and interest up to $25,000 per year, and its Tax Resolution Team will represent you to resolve the issues quickly. Note that if you do get a penalty from the IRS you have 15 days to send it to QuickBooks.

Health benefits administration

If you’re looking for payroll software that can do a little extra for you, QuickBooks may be the right one. You can take advantage of health benefits administration and deductions, which are traditionally only included with HR management software. This could save you the expense of onboarding a separate HR software in conjunction with your payroll software.

QuickBooks Payroll

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on QuickBooks's website

A version of this article was first published on Fundera, a subsidiary of NerdWallet.