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QuickBooks vs Paychex

QuickBooks vs Paychex

QuickBooks and Paychex are two of the longest running business software companies. QuickBooks was launched in the 1990s while Paychex has existed since before the internet and dates back to the 1970s. QuickBooks helps your business simplify complex bookkeeping tasks and track income and expenses. Paychex, on the other hand, helps manage the payroll side of your business and lets you accurately and efficiently pay employees.

How They Help Your Business QuickBooks Online vs Paychex

Benefits of QuickBooks

The primary benefits of QuickBooks are its small and medium-sized business bookkeeping features. These bookkeeping features are guaranteed to simplify business management. QuickBooks also uses the cloud, which means that you can access vital business information from any internet-connected device – including your smartphone.

Editor’s Note: Looking for information on payroll services? Use the questionnaire below and our vendor partners will contact you to provide you with the information you need:

Track income and expenses: QuickBooks lets you easily see your business’s revenue and expenses. You can track income over defined periods of time.

Automatic bank account synchronization: QuickBooks automatically syncs with your bank account and credit card accounts, which means all transactions made will be automatically shown in your QuickBooks account.

Additional bookkeeping features: QuickBooks can scale to meet the needs of your business. If your business already uses bookkeeping software and payroll software, then you won’t need the highest level QuickBooks plan. At the highest level, QuickBooks functions as both a bookkeeping platform and payroll software. Quickbooks offers a free 30 day trial.

Business reports: QuickBooks automatically prepares and prints business reports. Users can print between 20 and 65 business reports each month depending on which plan they chose.

Easy accountant access: When tax season arrives, you may want to give your accountant access to QuickBooks. QuickBooks allows for multi-user support and also has a unique accountant access function where up to two accountants can be added to your plan.

Benefits of Paychex

Paychex focuses on the payroll solutions side of business management. It offers personalized, one-on-one payroll service and lets users submit payroll data online, by phone, or over fax.

Paychex’s interface can be complicated to use and its mobile apps aren’t as powerful as some of the other payroll companies out there. It’s also more expensive than its competitors. However, what it lacks in a flashy user interface it makes up for in accurate, efficient payroll management:

Pay all different types of employees: Paychex lets you easily pay W-2 employees and 1099 contractors.

Multiple payment types: You can pay employees based on an hourly rate or based on salary data.

Multiple payment methods: Users can pay employees via direct deposit or by mailed check.

Multiple submission methods: File payroll data online using the Paychex web platform. Or, file it over the phone or using a fax machine.

Tax accuracy guarantee: Paychex guarantees that all payroll taxes you file will be accurate and filed on-time.

Tech support: Tech support is one of the biggest advantages of Paychex. Users receive a dedicated one-on-one payroll specialist assigned to their account. You can contact tech support during normal North American business hours.

QuickBooks Online vs Paychex Supported Services

Mobile apps: Both Paychex and QuickBooks offer mobile apps. Paychex’s mobile apps can be downloaded by employees and will display paystub data. QuickBooks mobile apps are feature-rich and let employers access and edit critical information about their business over the cloud.

Printed paychecks: QuickBooks supports printed paychecks through Intuit Online Payroll, while Paychex supports printed paychecks only when mailed to your office (you can’t print out your own paychecks with Paychex, but you can with QuickBooks).

Phone support: QuickBooks does not allow for payroll data entry over the phone, while Paychex does.

Cloud support: All Paychex data is hosted on the company’s servers can be accessed over the internet. QuickBooks is fully supported by cloud servers and can be accessed and edited real-time from any internet-connected device.

Compatibility: QuickBooks and Paychex are compatible with one another and information will sync across platforms.


Paychex customizes its pricing to each individual user and does not offer specific pricing packages. If you want to learn more about Paychex’s pricing, you’ll need to contact a sales rep directly. The sales rep will create a custom quote for your business. Typically, Paychex is two or three times more expensive than its competitors.

Other Points of Comparison QuickBooks Online vs Paychex

Pricing: Paychex and QuickBooks cater to two types of customers. Paychex is designed more for larger businesses with dedicated payroll and accounting staff. QuickBooks, on the other hand, caters more to small and medium-sized businesses with tighter budgets. As a result, pricing is considerably higher with Paychex than it is with QuickBooks.

User interface: Paychex has a notoriously difficult online interface. It’s complicated and packed with information. It’s not impossible to learn, but it will take a few payroll periods to make everything seem natural. QuickBooks is the total opposite and has a colorful, user-friendly UI.

Tech support: Paychex has some of the best tech support services in the industry. The most valuable part of Paychex’s tech support is the dedicated payroll specialist assigned to your account, who can answer any questions you might have. QuickBooks also has call center staff available and online help tutorials, but tech support isn’t nearly as personal.

Submit payroll data by phone or fax: Some businesses don’t like submitting payroll data online. If that’s the case with your business, then Paychex is likely the best option. Unlike other modern payroll service providers, Paychex doesn’t force users to submit payroll data online. Instead, they can submit payroll data by phone or by fax.

Ease of use: Paychex can be a complicated online platform to use. It has a steep learning curve and can’t be mastered in a few hours. QuickBooks can also be intimidating to use for the first time but has a gentler learning curve and a simpler introductory process. If you or your staff aren’t good with computers, then Paychex may be more difficult and time-consuming than you bargained for.

Employee hour submission: Paychex does not allow your employees to report their own hours. QuickBooks allows employees to report their own hours through Intuit Online Payroll, but the service costs extra.

Our Verdict On QuickBooks Online vs Paychex

Paychex is designed to perform a single role: pay employees efficiently and accurately. Paychex is very good at that – although it tends to be more expensive than its competitors.

QuickBooks, at its heart, is a bookkeeping platform that simplifies income reporting and expense tracking. However, the more you pay for QuickBooks, the more services you receive. On the highest level QuickBooks plans, users can choose to pay an additional fee to add Intuit Online Payroll to their accounts, which effectively turns QuickBooks into a unified payroll/bookkeeping solution.

If you want to use two different services for your payroll and bookkeeping, then Paychex is a good choice. If, however, you want to sync business bookkeeping information across platforms, then QuickBooks is an excellent choice – due largely to its automatic syncing with Intuit Online Payroll.

That being said, Paychex can sync information with QuickBooks and there’s nothing preventing you from using both Paychex and QuickBooks to manage your business. Yes, Paychex is a more expensive solution, but it provides a personal level of service we don’t see with most other payroll processing platforms.

If you’re managing a larger business and anticipate needing tech support to solve payroll-related problems, then Paychex may be worth the extra cost. If you’re a self-starter who likes to solve problems on their own and manage your business from any internet-connected devices, then QuickBooks may be the better option.

Editor’s Note: Looking for information on payroll services? Use the questionnaire below and our vendor partners will contact you to provide you with the information you need:

About Johnson Hur

After having graduated with a degree in Finance and working for a Fortune 500 company for several years, Johnson decided to follow his passion by embarking on a path to the digital world. He has over 8 years of experience with large companies setting marketing strategy.


  1. This content is great! It definitely hits a pain point of a lot of startups and small businesses when they are trying to figure out the best accounting software for their company. After choosing QuickBooks, having a walk through the intricacies was important and extremely helpful.

    • Thank you for your feedback Roman! I agree with you 100% that finding the right accounting software can be a big pain point for a small business.


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