QuickBooks vs Paychex

October 1, 2023

QuickBooks Payroll vs Paychex Flex: An Overview

Is Paychex the best way to pay, or will QuickBooks get it done quicker? Questions like this are at the forefront of every small business owner’s mind as they wrestle with a very important decision. 

You may have heard of QuickBooks Payroll – the latest addition to what is known as one of the best bookkeeping software out there. It adds payroll management on top of the existing bookkeeping function. But can the folks at QuickBooks beat one of the most economical and scalable dedicated payroll providers?

Getting a good HR and Payroll Management software will make the life of any small business owner easier. I have reviewed nearly 70 different payroll software. Here is what I’ve discovered about these two.

QuickBooks Payroll 

Features Overview

Paychex Flex

Features Overview

Multiple Authentication Factors

Extensive Cybersecurity Protocols

Payroll Processing Y Y
Direct Bank Disbursement Y Y
Tax Calculations and Filing Y Y
Payroll Compliance Y Y
Mobile Apps Available Y Y
Employee Self-Service N Y
Accounting Integration Y N


QuickBooks Payroll vs Paychex Flex: Features

QuickBooks has the following main features.

  • Payroll Management and Automation

QuickBooks Payroll features a paycheck calculator that automatically determines how much to pay. It grabs the pay time, rate, bonuses and overtimes, state and federal taxes to generate the pay. Then the payrolls can be printed or directly deposited.

  • Same Day Direct Deposit

If you submit the payroll before 7 am, the money will be deposited into your employees’ accounts on the very same day.

  • Auto Taxes and Penalty Protection

Taxes will be automatically calculated, filed, and paid. If QuickBooks makes any mistakes, they will reimburse you for the penalty of up to $25,000. This is a great inclusion, especially if you have a small business that cannot afford a big penalty.

  • Time Tracking

QuickBooks Payroll has excellent timesheets, tracking, and scheduling. Everything can be done through the mobile app as well. It can integrate with other scheduling software. One can even set up Geofencing to detect non-overtime employees who are still at the office after hours. 

  • Help and Resources

QuickBooks has plenty of tools to help a new business owner get used to HR. For example, a glossary helps them figure out common phrases and terms, while the Tax Map is a great tool for navigating the maze of state tax laws.

Paychex Flex has most of the same features, albeit with some differences.

  • Payroll Services

Paychex Flex has flexible payroll processing on both mobile and desktop. The dashboard is highly configurable and employees can also self-service. Highly robust data analytics is available, which is great for medium businesses for optimization.

  • Payroll Tax Services and Tax Credits

Calculates and pays taxes automatically. It also makes sure your taxes have been filed with the correct organization. Additionally, Paychex Flex will search for Tax Credits for you for savings. If you have a small business, you will definitely want all the savings you can get.

  • Time Tracking

Paychex Flex’s time tracking features are very similar to that of QuickBooks. However, it has many more options for employees to ‘Punch-In’, such as through a web portal, app, kiosk, or biometric or voice scans. It gives you a lot of options and flexibility for time tracking when you have a lot of employees in different roles.

  • Resources and Training 

New users get to work one-on-one with a Paychex HR setting up. This is an excellent opportunity for beginners to learn about HR. You can keep getting experience advice even after setting up.

QuickBooks has the advantage of same-day direct deposit and penalty protection. However, those two are features you won’t need very often. 

There isn’t much of a difference between payrolls being disbursed later the same day versus the next day, unless you are bad at planning things out. And tax penalties should be very rare, as the goal of the software is to avoid them in the first place.

So, we would choose Paychex Flex’s features over QuickBooks’ for small and medium businesses.

Winner: Paychex Flex

Visit Paychex


QuickBooks Payroll vs Paychex Flex: Plans and Pricing

Pricing is very important for any business owner to consider. The Payroll system should not cost more than the time and money it saves you.

QuickBooks Payroll cannot be purchased independently. In order to use it, you must purchase a QuickBooks plan as well. The plans range from $25 to $180 a month.

Once you get a Quickbook plan, you can add a Quickbook Payroll plan to it.

  • The Core plan costs $45 plus $4 per employee monthly. It includes all payroll features, health instance, 401(k) and 1099 filing.


  • The Premium plan costs $75 plus $8 per employee monthly. It adds workers compensation, expert HR support and same-day deposit.


  • The Elite plan costs $125 plus $10 per employee monthly. It adds expert setup and 

On the other hand, Paychex Flex’s pricing is not clearly given.

Paychex Flex Essentials starts at $39 plus $5 per employee monthly. It includes all the basic features described above. 

There are two additional plans: Select and Pro. However, they require price quotations. They add features such as Unemployment Insurance, Garnishment, and Onboarding. While these are great features to have, they are not completely essential for small businesses and you must decide if they are worth it or not. 

Overall, QuickBooks Payroll loses out on virtue of the fact it forces you to purchase the bookkeeping software first. There are other alternatives to QuickBooks for accounting, such as Xero or FreshBooks. Since those are cheaper, you can save more by combining them with Paychex Flex.

Winner: Paychex Flex 

Visit Paychex


QuickBooks Payroll vs Paychex Flex: Ease of Use and Setup

Ease of use is another critical point small and medium business owners need to mind. Ideally, the goal is to switch to this payroll system with minimal disruption to the daily running.

That means it should be quick and easy to implement the new system. The system should either be simple enough that there are no crucial mistakes to make. Or it should be robust and flexible enough that any mistakes made can be fixed quickly.

In terms of setup, QuickBooks offers guided tutorials on their website. There are training videos available for each of these steps. The detailed training videos are a great way to start.

The user interface of QuickBooks is more spacious than the Paychex Flex interface. The minimal design of Quickbooks is better for beginners, while Paychex’s more detailed and packed interface should be appreciated by experienced users. 

It is possible to get expert advice from QuickBooks. This is typically a separate service and each Pro Advisor will charge you for consultations. Training classes for both QuickBooks and Quickbook Payroll are only available on higher price tiers.

On the other hand, Paychex Flex offers a guided walkthrough from veteran HR personnel to help new users get started. They also offer a dedicated payroll specialist to work with you from the second tier, which should be relatively affordable.

Both QuickBooks Payroll and Paychex Flex have mobile apps. The QuickBooks Payroll mobile app is mainly suitable for carrying out payroll and admin work – create paychecks, set reminders and view history.

The Paychex Flex app, on the other hand, is for both employers and employees. The former can carry out payrolls, go through health benefits features, load any health and spending information, etc. 

Employees can check their W2s and stubs, any upcoming time-off or compensation, insurance details, balances and more. It can also be used for timekeeping, as employees can punch in through the app. The Paychex Flex app is simply more feature-complete.

Winner: Paychex Flex 

Visit Paychex


QuickBooks Payroll vs Paychex Flex: Security

Security is a prime concern in any business. A lack of security could expose potentially harmful and damaging information regarding your employees. For instance, any medical information must be kept perfectly strict and confidential, under the HIPAA.

If a business fails to keep employee or customer records safe, they may be liable and face legal action. We don’t want this to happen, so we hope you choose the most secure payroll and HR platform.

In QuickBooks, all customer data is hosted on local servers. The servers are highly secure, with 24/7 security staff, surveillance, and alarm systems.

The IT staff are regularly trained and drilled on Cybersecurity measures. Every single user activity is recorded in the Always-On Activity Log and Audit Trail features.

QuickBooks uses 128-bit SSL encryption and firewall, password-protected servers. This level of security is on par with those of Banks and financial institutions.

Paychex Flex’s security consists of multi-factor authentication from the user’s end. The employees are trained to recognize and respond to security issues and threats. This applies to both the Cybersecurity and Physical Security teams.

Overall, both have very good security. However, we give the edge to QuickBooks for having more detailed security measures.

Winner: QuickBooks Payroll

Visit Quickbooks


QuickBooks Payroll vs Paychex Flex: Customer Support

Running complicated software such as an HR and Payroll platform isn’t straightforward. There are plenty of issues that could crop up. It could be a legitimate error or mistake in the software, or the user simply not understanding how to carry out an action.

Since such mistakes could be very costly, we emphasize the importance of good customer support.

QuickBooks Payroll prefers to direct users to guided tutorials rather than dedicated customer support. The range of FAQs is extensive and covers nearly all possibilities.

The full list of support options includes video tutorials and webinars, a community message board, a resource center, and expert advisors.

To contact QuickBooks’ customer support, you have to log in and go to ‘Contact Us’. Then you may chat with an expert.

Support is available 24/7 in English, French, Italian, Spanish, and Chinese.

Paychex Flex is more upfront about offering expert services as part of their customer support. You can talk to an expert at any time you like, ranging from the initial startup to any concerns later on. 

The support is specialized into Admin, Employee, and Login support. Support is not restricted to online-only either. You may visit any one of the 100+ Paychex offices to get hands-on support. Phone support is available 24/7 as well.

Due to the extensive FAQs and more support options, we give this round to QuickBooks. The dedicated personal support of Paychex Flex does deserve an honorable mention, though.

Winner: QuickBooks Payroll

Visit Quickbooks


The Bottom Line on QuickBooks Payroll vs Paychex Flex

QuickBooks is the way to go for businesses that prefer to have better security and support in the background. While it has some standout features such as large reimbursements and great accounting integration with its own accounting software, it also has shortcomings.

For starters, QuickBooks simply is not a good value for the money. Most of its special features are not very useful, and are only available at higher-end plans, while other platforms offer all basic features at much lower prices.

Paychex Flex is more feature-rich and is better value for the money. Its standout feature is the dedicated, expert support it provides at all times, no matter what. While the rest of the support system may not be as good, this feature has the potential to cover any shortcomings.

If you prefer personal support over written guides, then Paychex edges out QuickBooks significantly. If you prefer written and video guides and FAQs, QuickBooks is a solid contender.

Visit QuickBooks Payroll!

Visit Paychex Flex!

Top 3 Payroll Services

Our Score
  • 1 month free trial
  • Trusted by over 200,000 businesses
  • All-in-one payroll and HR solution
  • Best for small businesses
  • “Autopilot” runs payroll itself
  • 3 months free with signup
  • Trusted by 850,000+ businesses
  • Dedicated customer service
  • Also offer HR and benefits management
  • 3 months FREE with signup
  • Trusted by 700,000 companies
  • Over 45 years of experience
  • All-in-one platform

What was covered on this page?

John Smithson

John Smithson

38, a small (but growing) business owner in the IT field.
I love to look for exciting and modern ways to keep my business ticking along, my employees happy, and most importantly, the business growing. I love researching the best software online to help me - and other businesses - achieve these goals.

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