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Intuit Online Payroll vs Paychex

Intuit Online Payroll vs Paychex

Intuit Online Payroll and Paychex are two of the longest-running payroll services in the industry today. Intuit debuted in the 1990s while Paychex dates back to the pre-internet days of the 1970s. With decades of experience, both Paychex and Intuit are fighting for your business. Today, we’re going to compare these two competitors and help you decide which one deserves your business. For our free payroll software guide, you can find it here.

Benefits of Intuit Online Payroll

Intuit Online Payroll is a simple, cloud-based payroll platform. It calculates employee payroll data and lets you accurately file necessary forms to the IRS. It guarantees accuracy for all state and federal taxes and will likely simplify your payroll process – even if you’re already using another payroll service provider.

If you need payroll software, Intuit Enhanced Payroll is exactly what you need. Intuit also offers a 30 day free trial and its only $2/ per additional employee.

Easily file payroll data: When you first subscribe to Intuit Online Payroll, you’ll need to manually enter employee data. Once you’ve done that, the software calculates all necessary deductions according to state and federal payroll tax law. Then, you can add more deductions based on employee agreements and company policies.

Hour data entry: Employees can add their own hours to the online Intuit platform every payroll period. However, this service costs extra and is not included on any of the basic Intuit plans. If you don’t pay the extra fee, you’ll need to manually enter hour information every payroll period.

Pay employees via direct deposit and printed checks: Once you’re finished entering payroll data for the week, Intuit lets you easily pay your employees. Payment is available via direct deposit and by printed check.

Accuracy guarantee: Intuit guarantees that all payroll taxes will be filed accurately and that all deductions are in accordance with the latest IRS regulations. All payroll taxes are also guaranteed to be filed on time.

Pay multiple types of employees: Intuit lets you pay multiple types of employees. The most basic plan only allows payments to W-2 employees, but the Enhanced plan, which costs $8 more per month, allows payments to both W-2 employees and 1099 contractors.

Benefits of Paychex

Paychex is a popular payroll system that has been around since the 1970s. It comes with a number of valuable benefits that will appeal to a specific niche group of businesses:

File payroll information online, by fax, or over the phone: Unlike most of today’s payroll system providers, Paychex accepts payroll submissions via fax lines and over the phone.

Tech support: Paychex assigns a dedicated payroll specialist to your account upon signup. You can directly contact this specialist if you have any questions.

Pay employees via direct deposit or printed check: Paychex lets you pay employees via direct deposit or printed check. You cannot, however, print off checks in your own office – checks will be mailed to you by Paychex every payroll period.

Hour data entry: Hour data entry must be handled by the employer, not the employees. There is no way for employees to enter their own data into Paychex.

Intuit Online Payroll vs Paychex Supported Services

Mobile apps: Intuit offers mobile apps for Android smartphones and tablets as well as the iPhone. Employers can manage most payroll information over this app and employees can view paystub data. Paychex also offers apps, but the apps only display paystub information to employees.

Printed paychecks: Intuit Online Payroll lets employers print their own paychecks. Paychex does not allow in-office printing, but users can have checks printed and mailed to their office.

Phone-based payroll submissions: Paychex lets you submit payroll data over the phone, if you wish, while Intuit forces users to submit payroll data online.

Cloud support: Intuit Online Payroll stores all data securely on the cloud, which means you can access the information anywhere. Paychex doesn’t use cloud computing, but all information is stored on its servers and can be remotely accessed online.

QuickBooks: Intuit and Paychex both automatically sync with QuickBooks.

Sage: Intuit does not sync with Sage, but Paychex does.

Paychex does not offer specific pricing packages. Instead, the company offers custom pricing packages for all clients. Paychex’s pricing is typically higher than its competitors – especially for smaller companies. Larger companies, however, may find bulk savings discounts are available. Contact a Paychex sales rep for more information.

Other Points of Comparison On Intuit Online Payroll vs Paychex

Methods of payroll submission: Intuit Online Payroll only lets users submit payroll data using one method – online submission. Paychex supports multiple submission options, including fax, phone, and online submission. If you prefer using phones and fax lines to submit payroll data, then Paychex may be the better option.

Methods of payment: Users cannot print off their own checks in-office with Paychex, but they can print off checks with Intuit. You can receive printed checks through Paychex over the mail, in which case they’re mailed from your closest Paychex office.

User interface: If you were to base your opinion of Intuit vs. Paychex on user interface alone, then Intuit would win and it wouldn’t even be close. Paychex’s online interface is dated and filled with confusing menus and information. It’s going to take a few payroll periods before you get used to the system. Intuit, on the other hand, offers an excellent user interface that is well-designed and built to be extremely easy to use.

Pricing and extra fees: Intuit charges an extra $2 per month per employee. Users also have to pay an extra $12 per month for each extra state in which they file payroll taxes. Paychex also charges an additional per-user fee and charges extra for additional states, but the specific amount changes from client to client. Since Paychex offers customized pricing packages, it’s difficult to compare the two providers head-to-head for pricing. However, Paychex is typically two or three times more expensive than other providers.

Tech support: When you compare Intuit’s tech support to most other payroll software providers’ tech support, Intuit usually wins due to its helpful tech support employees and online database of valuable information – including tutorial videos. However, Paychex offers equally excellent tech support and tutorials. When you sign up for Paychex, you get a payroll specialist who is dedicated to your account. That’s a huge benefit for anyone who appreciates personalized one on one support.

Our Verdict On Intuit Online Payroll vs Paychex

Paychex is significantly more expensive than most other payroll solutions available today, but that extra price comes with added benefits. The major benefit of working with Paychex is the high-quality tech support. Users receive a personal one-on-one payroll specialist who can answer any questions they might have about their account or employee payroll data. Paychex also includes unique features like the ability to submit payroll data over the phone or via fax.

Paychex, however, lacks many of the features that have made Intuit popular. Paychex doesn’t have full-featured mobile apps, for example, nor does it allow users to print off their own paychecks. It also has a complex, aging online interface that can be difficult to use.

Intuit Online Payroll, on the other hand, is a cloud-based online payroll program that doesn’t have the same personalized support as Paychex, but offers accurate payroll tax calculations for a fraction of the price of its competitor. Its mobile apps can be used to edit payroll data online over the cloud and employees can choose to enter their own information online (for a small added monthly cost).

If budget is not an issue for your company, then you may want to consider Paychex. However, if budget is a major concern, then the high price of Paychex makes it a poor option for many of today’s businesses. In most cases, Intuit Online Payroll is simply the better option for today’s small and medium-sized businesses.

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. Paychex does allow the employers to print their own checks on-site. Their new User Interface “Flex” just won the AICPA “Perfect” award for ease of use, along with scores of other accolades. Paychex does not charge extra for filing in multiple states. The apps are full-featured and can allow the employer to run payroll from their mobile. Is it really a good idea for employees to log their own hours?

  2. 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 payroll software for their company. After choosing Intuit, having a walk through the intricacies was important and extremely helpful.

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


  3. I have a small fleet claim processing business with 7 employees. I still use QuickBooks + Enhanced Payroll.

    Based on my experience, it’s very hard to know which software is good until you are well deep into it. A good payroll service should address each of the following.

    Integrated w/ bookkeeping software
    tax tables subscription (Federal & State)
    print checks and stubs
    Print Federal tax forms
    Print State tax forms
    e-file Federal forms
    e-file State forms
    e-pay Federal taxes
    e-pay State taxes (for states that have the option)
    direct deposit option

    Once your efile/epay accounts have been established with the IRS and your State, your payroll software should be able to automate it.

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