How To Do Payroll In QuickBooks In 5 Easy Steps

Ready to start using QuickBooks but don’t have time to get into the technical weeds? This article has the simple explanation you need to start quickly running payroll in QuickBooks Desktop. Follow the five simple steps below and you’ll be paying employees in no time.

Looking for QuickBooks Online payroll instead? Here is our complete step-by-step guide on how to run payroll in QuickBooks Online.

Benefits Of QuickBooks Desktop Payroll

For many business owners, payroll is a time-consuming task that requires a high degree of precision. From staying abreast with the latest laws in taxation and employment to navigating the rules of taxation agencies, doing payroll yourself can become overwhelming fast.

Fortunately, payroll software can help you make sure you’re paying your employees the right amount, on time. The biggest benefits that come with payroll software such as QuickBooks Desktop Pro include:

• Full-service payroll tax preparation with automatic tax calculations, filing, and payments
• Employee information such as pay rates and employment status organized in one place
• Easy management, tracking, and definition of employee benefits
• Payday reminders that keep you from missing payment deadlines

Long story short: QuickBooks Desktop Pro may be the payroll management software for you if you’re struggling to run payroll yourself. QuickBooks Desktop automates tons of payroll processes, prevents you from making mistakes when processing your employees’ pay, and makes sure your business can continue to grow without running into IRS-related hiccups.

If you’re interested in implementing QuickBooks Desktop as part of your business’s payroll process, then read on to quickly set up your new software and start running payroll like a pro!

Before You Start Running Payroll In QuickBooks

Setting up payroll in QuickBooks, though, can be a bit complicated for the uninitiated. Take a look at our quick guide to setting up payroll in QuickBooks if you need help getting started.

After you’ve set up your business’s payroll, there are two things you’ll need to do before running your first pay cycle:

1. Enter employee hours
2. Create a bank account

To run your payroll, first make sure that all of your employees have recorded their time within QuickBooks. If you need help with this, check out How To Track Time In QuickBooks.

You’ll also want to make sure that you’ve added the business bank account you pay employees from into QuickBooks. To learn how to do this, read How To Add A Bank Account To QuickBooks.

Once these two steps are complete, you’re ready to get started!

How To Process Payroll In QuickBooks

Running QuickBooks Payroll is easy enough once you’ve set up your payroll, banking, and employee time tracking correctly. Before your next pay cycle, navigate to the payroll center and follow the steps below to run your payroll and get your employees paid.

1. Navigate to payroll in QuickBooks
2. Choose the type of payroll to run
3. Enter payroll information
4. Review and create paychecks
5. Confirm payroll

Step 1: Navigate To Payroll In QuickBooks

To begin, go to ‘Employees’ at the top left of your screen, select ‘Payroll Center’, and click ‘Pay Employees’. If it’s your first time using QuickBooks Desktop Pro, you should be taken to a screen that looks like this:

Click “OK, I’m ready!” to get started.

Step 2: Choose The Type Of Payroll To Run

You’ll need to decide whether to run an unscheduled or scheduled payroll shown in the below photo before you can start entering your payroll information. Starting an unscheduled payroll will immediately take you to the screen shown under Step 3.

Running a scheduled payroll also takes you to the screen shown under Step 3 but first requires that you assign one or more specific employees to a payroll schedule. To do this, navigate to the ‘Employees’ tab shown on the very left-hand side in the below photo. Select the name of the employee(s) who you wish to assign to a payroll schedule, navigate to their ‘Payroll Info’ tab, and assign them a payroll schedule from the ‘Payroll Schedule’ dropdown list.

Step 3: Enter Payroll Information

Enter all of your payroll information, beginning with the pay period end date and check date. Select the bank account you want to pay employees from (QB will show you the existing account balance). Select whether you will print checks using QuickBooks or if you are going to handwrite your checks.

The most important part of entering payroll information is to select which employees you want to pay and review their hours to make sure everything looks right before proceeding. You can select as many employees as desired, so long as you’ve assigned them to a payroll schedule. Click “Continue” when ready.

Step 4: Review & Create Paychecks

Next, review the information to make sure everything looks correct. QuickBooks will tell you how many paychecks will be issued on the left-hand side, underneath ‘Payroll Information’. It will also total up the gross pay, taxes, deductions, net pay, employer tax contributions, total hours, and direct deposit amounts for the pay period. After you review all of the information, click “Create Paychecks.”

Step 5: Confirm Payroll

Congrats! You’ve officially run payroll in QuickBooks Desktop Pro.  This screen will tell you how many paychecks have successfully been created, how many are ready for printing, and how many are ready to be directly deposited.

From here, you can print your employees’ checks or send your payroll in for direct deposit processing and print the pay stubs for your direct deposit employees. If you have any troubleshooting issues, check out the QuickBooks Payroll Help Centers or call QuickBooks payroll support directly.

How To Use The New Coronavirus Features In QuickBooks Payroll

In the wake of COVID-19, QuickBooks Desktop now offers employers the option to provide employees paid leave if they’ve been affected by the pandemic. Follow the below steps to ensure your employees get the money they need in compliance with the Family First Coronavirus Response Act (FFCRA).

QuickBooks’ website indicates that, depending on factors such as the employee benefits you offer and the hourly rates you pay, you need to square away a few things first before they can provide paid leave and sick time for the coronavirus. Employers should make sure to review these steps before trying to pay their employees paid leave and sick time for COVID-19 in QuickBooks Desktop.

Step 1: Set Up Paid Leave Items

To begin, navigate to ‘Employees’ at the top left of your screen in QuickBooks Desktop (you can do this from any page in your software). Click it, hover over ‘Manage Payroll Items’, then select ‘View/Edit Payroll Item List’. 

Step 2: Select A Paid Leave Item

A screen containing the different National Paid Leave items in QuickBooks should appear. Double-click the paid leave item you want to set up, rename the item if desired, and click ‘Next’.

Step 3: Set Your Taxability To Unmark Social Security

Select ‘Next’ until you’re on the ‘Taxable Compensation’ screen. Once there, select the ‘Default’ button to designate your taxability as unmarked for Employer Social Security. Repeat this process for each National Paid Leave item that you set up.

FAQs About How To Do Payroll In QuickBooks Desktop

Still Have Questions About QuickBooks Payroll?

Looking for a more detailed instructions on how to properly handle QuickBooks Payroll? We answer all of your questions in our Complete QuickBooks Desktop Guide.

Confused by other QuickBooks features? QuickBooks Desktop Pro has quite a few bells and whistles to guide users who need to run payroll, and it can be tough to know which ones to use and when.

Overwhelmed by QuickBooks Pro and ready for a change? It may be time to switch to QuickBooks Online. Our complete review of QuickBooks Online guides you through its easy-to-use features and cloud-based, affordable platform. Best of all, you can easily import your QuickBooks Desktop data into QuickBooks Online.