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How to Fix QuickBooks Payroll Taxes Are Calculating Incorrectly Issue?

QuickBooks Payroll Taxes are calculated incorrectly due to reasons

QuickBooks Payroll Taxes are calculated incorrectly due to reasons such as outdated Payroll Tax Tables, misconfigured/inactive Automatic Calculation Features, low gross wage, incorrect Payroll Item settings, or exceeding annual legal limits.

QuickBooks Payroll not calculating taxes correctly error can be dealt with, but the user first needs to understand the cause(s) behind the error. And then, depending on the cause of the error, the user must follow the appropriate steps to fix the error.

For instance, in case the outdated version of Payroll Tax Tables (PTT) is causing the disparity in the payroll calculations. The user needs to acquire the latest version of payroll tax tables to solve the error.

What are the cases when QuickBooks Payroll is not to Take Out Taxes?

The following are the root causes behind QB Payroll not calculating taxes correctly:

  1. Low Gross Wages: The employee’s gross wages from the last payroll might be too low.
  2. Outdated Payroll Tax Table: The Payroll Tax Table is outdated, which is leading to problems in the calculation process.
  3. Malfunctioning Automatic Calculation Feature: The feature for automatic calculation is either not set up correctly or not activated, resulting in taxes being calculated incorrectly.
  4. Improper Payroll Settings: The sequence of Payroll items is incorrect, or the settings of Payroll items (particularly those related to quantity or hours) are not set up properly, thereby impacting important calculations.
  5. Surpassed Annual Limit: There is a legally defined limit for withholding payments associated with deductions, contributions, vacations, and sick leave under state and federal laws. If this limit is surpassed, it signifies an error that leads to inconsistencies in the payroll calculation.
  6. Payroll not updated: The software is not updated to its latest version.

Solutions to Fix the “QuickBooks Payroll Is Not Taking Out Taxes” Issue

Complete the following set of solutions to handle payroll tax errors:

Correct year-to-date and quarter-to-date wage or tax information of the employee

To view and correct the taxes of all active employees in an employee withholding report, complete the following steps:

  1. Step 1: Select Reports.
  2. Step 2: Navigate to Employees and Payroll.
  3. Step 3: Click on Employee withholding.
  4. Step 4: Click on the Customize Report tab.
  5. Step 5: Select the columns as needed.
  6. Step 6: Click on the items you want to display in the report in the display list section.
  7. Step 7: Click OK to save changes.
  8. Step 8: Check if your employees are set up correctly for state, local, and federal taxes.
  9. Step 9: To edit the employee info window, double-click the Employee’s name.
  10. Step 10: Click on Payroll info.
  11. Step 11: Click on the Taxes tab.
  12. Step 12: Click on the Federal, state and/ or Other tab.
  13. Step 13: Make sure that the employee is marked correctly for taxes and exit to complete the process.

By Optimizing Employee Paycheck Calculations and Manual Tax Entries in QuickBooks Payroll

If you have a QuickBooks payroll subscription, you can save the employee’s paycheck based on previous calculations. Change the Check details of the employee for accurate calculations. Manually enter both the Withholding and Employer matches in QuickBooks payroll. 

If you have subscribed to the assisted version of payroll, you might face issues due to the Payroll Taxes being filled by Intuit.

To resolve the error, update the QuickBooks software to the latest version. This will sync the software with the latest payroll forms and tax tables. Before you run the payroll, check if the Employees and Payroll items have been set up correctly.

Verify The Setup Of The Item For the Annual Limit

Check if the annual set limit has been exceeded. If a payroll component isn’t accurately computed and ceases to be calculated on a salary slip, it could be due to the fact that the annual limit or the default limit of the employee has been maxed out. 

To access and verify the setup of the item, complete the following steps:

  • Step 1: Navigate to Lists and Payroll Item List from the main menu.
  • Step 2: Right-click on the payroll component you want to change and select Edit Payroll Items.
  • Step 3: Scroll to the subsequent screen until you arrive at the Limit Type screen.
  • Step 4: Ensure that the checkbox at the bottom is marked.
  • Step 5: If the limit is correct and has been exceeded, the employee’s payroll should stop calculating at that limit. Update the amount of the limit as needed.
  • Step 6: Under Limit Type, verify that you have chosen the right option.
    • Annual – Renews every year
    • Monthly – Renews every month
    • One-time limit
  • Step 7: You can change the default limit or Limit Type selection to suit your needs.
  • Step 8: Click on Finish to save changes and complete the process

Revert Employee Paychecks after Reviewing Employees Tax Setup

Review the tax setup for each employee as it influences how QuickBooks calculates taxes. Revert the employee’s paycheck to refresh the payroll data and recalculate the taxes on the transaction. Follow the below steps to accomplish this:

  1. Step 1: Open the Employee’s payroll information.
  2. Step 2: Right-click on the Employee’s name highlighted in yellow.
  3. Step 3: Select the “Revert paycheck” option.

Update QuickBooks Desktop to Latest Release then Get Payroll Updates

Make sure your QuickBooks software is up-to-date, then complete the following steps to get QuickBooks Payroll updates:

  1. Step 1: Launch QuickBooks.
  2. Step 2: Click on Employees.
  3. Step 3: Select Get Payroll Updates.
  4. Step 4: Choose the Download entire payroll update radio button.
  5. Step 5: Click on Update.

Wait for the update process to complete. Once the update is successful, try running your payroll again to ensure the taxes are calculated correctly.


Q. Why aren’t taxes deducted from my paycheck?

There could be several reasons why taxes aren’t being deducted from your paycheck, such as a mistake in the payroll configuration, inaccurate employee details, or new tax laws.

Q. How can I correct the federal tax withholding in QuickBooks?

To adjust the federal tax withholding in QuickBooks, you need to navigate to the employee’s profile, modify the W-4 form, and update the tax withholding details.

Q. What does it mean when QuickBooks payroll isn’t calculating taxes?

An employer deducts a portion of the employee’s salary or wages from the paycheck to pay to the government as taxes. If this amount isn’t deducted from the paycheck even when the employee is above the minimum threshold in QuickBooks, it means there’s an error or problem with QuickBooks Payroll.

By : January 22, 2024
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