How To Run Manual Payroll In QuickBooks?


Running payroll is an essential task for businesses of all sizes. QuickBooks, the popular accounting software, offers both automated and manual payroll options. While automated payroll simplifies the process, there are situations where running manual payroll in QuickBooks becomes necessary. In this article, we will explore how to run manual payroll in QuickBooks and guide you through the step-by-step process.

Understanding Manual Payroll in QuickBooks

2.1. What is Manual Payroll?

Manual payroll is a method of processing payroll without relying on QuickBooks’ automated features. With manual payroll, you have more control over each aspect of the payroll process, including entering employee hours, calculating deductions, handling taxes, and generating paychecks.

2.2. Why Use Manual Payroll in QuickBooks?

There are several scenarios where using manual payroll in QuickBooks can be beneficial. For example, if you have unique pay structures or compensation arrangements that cannot be easily handled by the automated payroll system, manual payroll gives you the flexibility to accommodate those complexities. Additionally, manual payroll can be useful if you only have a few employees and prefer a hands-on approach to payroll processing.

Setting Up Manual Payroll in QuickBooks

To start running manual payroll in QuickBooks, you need to configure a few settings and set up the necessary payroll items and employee information. Follow the steps below to get started:

3.1. Enabling Manual Payroll

To enable manual payroll in QuickBooks, go to the “Edit” menu, select “Preferences,” and choose “Payroll & Employees.” In the “Company Preferences” tab, uncheck the option for “Full Payroll” and click “OK” to save the changes.

3.2. Creating Payroll Items

Next, create the payroll items required for manual payroll processing. These items include wages, bonuses, deductions, and taxes. Define each payroll item by specifying its name, type, and associated accounts.

3.3. Adding Employees and Their Payroll Information

Once the payroll items are set up, add your employees’ information into QuickBooks. Include details such as their names, addresses, Social Security numbers, and wage rates. You can also specify any additional payroll information, such as exemptions, deductions, and benefits.

Running Manual Payroll in QuickBooks

Now that you have set up manual payroll in QuickBooks and added the necessary information, you are ready to run payroll. Follow the step-by-step process outlined below:

4.1. Entering Employee Hours and Earnings

Start by entering the hours worked by each employee during the payroll period. You can input this information manually or import it from a time-tracking system if you have one integrated with QuickBooks. Once you have entered the hours, calculate the gross earnings for each employee based on their wage rates.

4.2. Calculating Employee Deductions

Next, calculate the deductions for each employee. This includes federal and state taxes, Social Security contributions, Medicare, and any other applicable deductions. QuickBooks provides tax tables and formulas to help you calculate these deductions accurately.

4.3. Handling Taxes and Other Withholdings

After calculating the deductions, ensure that you accurately withhold the necessary taxes from each employee’s paycheck. This includes federal and state income taxes, as well as any local taxes applicable to your business location. QuickBooks can assist you in calculating and withholding the correct amounts.

4.4. Generating Paychecks

Once you have entered the necessary information and verified the calculations, it’s time to generate paychecks for your employees. QuickBooks allows you to preview the paychecks before finalizing them. Review the amounts and verify that everything is accurate before printing or distributing the paychecks.

Reviewing and Adjusting Manual Payroll

5.1. Verifying Payroll Reports

After running manual payroll, it’s crucial to review the generated payroll reports to ensure accuracy and compliance. QuickBooks offers a range of payroll reports that summarize employee wages, taxes, and deductions. Take the time to review these reports and compare them to your records to identify any discrepancies.

5.2. Making Adjustments

If you discover any errors or need to make adjustments to the payroll calculations, QuickBooks allows you to do so easily. You can edit individual employee records, update hours, adjust deductions, or make any other necessary changes. Remember to double-check the calculations after making adjustments to ensure the accuracy of the payroll.


Running manual payroll in QuickBooks gives you more control over the payroll process and allows for customization to meet specific business requirements. Learn more

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