Payroll Options for QuickBooks

payroll quickbooks desktop quickbooks online Oct 30, 2021

 If you have employees, Payroll is a huge part of your business. There are so many aspects of Payroll, it's a full-time job (get it?). It's much more than calculating paychecks. There are benefits and compliance issues when you have employee. There are a variety of Payroll services. Some are deeply integrated into Quickbooks, some are standalone options. Choosing the right service depends on what you need. We have created a Payroll Chooser to help guide you based on your needs. We also have a course that is available in all of our memberships that is Choosing the Right Payroll Service. Below are some of the highlights of the different Payroll offerings.

Desktop or Online

If you are using QuickBooks, there are integrated Payroll services that can be activated so you can run payroll directly inside your company file. Using one of the options might be a good idea if job costing is a high priority. The closer the integration the better reporting functionality if you need the payroll accounting to impact other areas of your business such as job profitability. There are other payroll options outside of the QuickBooks Payroll offerings that can handle this task as well so don't count them out if other business needs are being met.

Security Concerns

When you have payroll directly running inside of your Quickbooks company file, other users who are in your company file potentially having access to payroll could be a concern. If you have Sales people or people doing other tasks seeing something they shouldn't is a concern for you and your company. Some versions of QuickBooks will have better security options than other to ensure wandering eyes don't see what they shouldn't. QuickBooks Enterprise has hundreds of customizable security roles as compared to QuickBooks Online which is not nearly as robust. 

Desktop Payroll Options

Inside QuickBooks Desktop there are two options for payroll. Enhanced and Assisted. The major difference between the two is what happens after paychecks are created. Once the paychecks are created, the payroll tax liabilities and Payroll Forms that need to be paid and filed will be initiated by the employer when using Enhanced Payroll. If you are using Assisted, Intuit will pay the taxes and file the forms for you. Other liabilities like retirement, garnishments, etc. are not paid by the service.

QuickBooks Online Payroll

There are three options for QBO Payroll, Core, Premium, and Elite. Each are full service payroll options where taxes and payroll forms are filed for you. There are features that distinguish each other, but not to worry, we have created courses for each of the online payroll options that covers each level of Payroll and the functionality tied to each. They are available in all of our memberships.



The most basic version of QB Online payroll is QuickBooks Online Payroll Core. It will offer full-service payroll, including automated tax and forms, auto payroll for salaried employees on direct deposit, and access to health benefits for you and your team. It is the only online payroll service that does allow you to opt out of the automatic tax payments and form filings to give you a little flexibility and control. The setup for this product is a self-guided setup with no assistance from Intuit. 


The version called Full Service, which is when Intuit pays the taxes for you will now be called QuickBooks Online Payroll Premium. This is a more robust version of Full Service. It features premium time tracking by QuickBooks Time to run payroll faster and bill more, expert setup review to ensure your setup is done right, and access to the Human Resource support center.  


Elite is a new product that adds robust features to the full-service payroll such as Prioritized help when you need it. 1:1 HR advisors support that can help you create a handbook,  Professional payroll setup done for you. It includes elite time tracking by QuickBooks Time which tracks project hours and labor expenses in real-time & GeoFence which alerts workers to clock in and out when entering and leaving the job site. Tax-Free penalty guarantee by Intuit.


Starting on or after March 1, 2020, all of the new features will be released into the existing products. Releasing the new features into the existing products will help make this transition as smooth as possible. There will be no disruption to your business processes and there will not be any data to transfer – all payroll history will be there. These updates will take effect after their billing date starting March 1, 2020. 


QB Online Payroll as a Standalone

It is possible to use any of the QB Online payroll services as a standalone service without using any QuickBooks accounting options. Core, Premium and Elite payroll can be activated individually. You can also export that to QuickBooks desktop or a separate QB Online company. If you don't already have QB Online, you can simply activate QB accounting in the payroll if desired, but if you really want to keep payroll separate, using QBO as standalone might be a good alternative. Just keep in mind that using a desktop product and an Online payroll service make be a little confusing and the navigation will not be consistent between the two.

Shortcomings of QB Payroll

QuickBooks Payroll services excel at integration, but there are a few things that they don't do. HR concerns, (employee handbooks, hiring, termination, compliance issues) are not strong suits. You really need to know what you want payroll to do in order to get the most out of QuickBooks Payroll. Retirement Service, health Benefits, workers comp, are also things that QuickBooks Payroll services are just now getting into. If these are concerns, you might want to look into an outside service that specializes in Payroll. 

Other Payroll Services

There are other Payroll services that promise they integrate with QuickBooks but require proper setup and may be problematic if the connection sends the data over more than once or is not mapped properly. However once the data comes over it is typically in summary form.  ADP, the industry leader in payroll has integration tools that work including options to bring over detailed job costing into QuickBooks desktop for an additional fee. They also have hundreds features you can add to your payroll solution making it your solution customizable as you grow.  ADP came on one of our Wednesday Workshops to talk about their payroll solutions.

If you would like to learn more tips and tricks, click here to access our entire course library!!

Course Library

Stay connected with news and updates!

Join our mailing list to receive the latest news and updates from our team.
Don't worry, your information will not be shared.

We hate SPAM. We will never sell your information, for any reason.