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QuickBooks Payroll Not Calculating Social Security

QuickBooks Payroll Not Calculating Social Security

Payroll accounting is a practice of keeping track of employee compensation, including benefits, payroll taxes, and other amounts deducted from wages. To get a clear picture of payroll costs and specifics about each transaction, such as the date of payment, the amount of pay, and the location of pay delivery, all this information is recorded in financial journal entries. A general ledger (GL) keeps track of financial transactions for financial reporting, and each journal entry is recorded.

If you’re struggling with ‘QuickBooks Payroll’s unable to calculate Social Security and Medicare’, this solution will assist you in resolving the issue. Take the necessary actions to rectify it and make QuickBooks payroll calculate social security and Medicare for you, saving you time and making your work easier. 

If payroll taxes aren’t being deducted from an employee’s pay, you’ll need to look at the order of the payroll items on the paycheck to see if that’s affecting the calculation. The first item in the ‘Other Payroll Items’ section of the ‘pay check’ should be that payroll item if you only want it to calculate based on the employee’s earnings. After any additions or deductions, if you want to include them in the calculation, add the payroll item. 

The next thing to do is to make sure the payroll item is configured to calculate based either on quantity, hours, or neither. The quantity or number of hours must be manually entered in the Quantity column of the ‘Preview Pay check’ window once a payroll item is configured to calculate based on quantity or hours.

We suggest adjusting the payroll item’s calculation settings as follows:

This is How:

  • Select Lists and Payroll Item List from the top menu bar.
  • To edit a payroll item, select Edit Payroll Item from the context menu of the right-clicked item.
  • When the Calculate Based on ‘Quantity screen’ appears, select Next. 
  • If this item does not need hours or quantity to calculate, change the setting to None.
  • Select Next Before clicking Finish
  • Press the Finish button.

After that, check to see if the annual cap has been set or reached. It may be indicated by a checkmark in the This is an annual limit checkbox and a default limit set that the employee has reached when a payroll item previously calculated correctly and stops doing so on a paycheck. Please carry out the actions listed below to verify this.

  • Select Lists from the top menu bar. After that, the pay stub item list.
  • Click Edit Payroll Item from the context menu of the payroll item you want to change.
  • When the Limit Type screen appears, select Next.
  • Verify that the right option was selected by looking below the Limit Type.
  • Adjust the Limit Type selection or the Default Limit as necessary.
  • Click Finish.

Check the accuracy of the limit in the bottom box. If the limit is accurate, the payroll item for the employee should stop calculating at this limit. Update the amount if the limit is incorrect.

Additionally, we also suggest examining previous paychecks to see if any payroll or Social Security and Medicare taxes were over-deducted. However, as soon as a previous tax return contains an incorrect deduction, the QuickBooks system will automatically make the necessary corrections. 

Social Security and Medicare taxes are calculated incorrectly for several reasons. Below are some of  the reasons:

  • QuickBooks is not updated, or the update encounters an internet outage.
  • utilizing a flawed rendition of the tax table.
  • Employee’s YTD is negative.

To fix the issue, let’s confirm that you can access version 21902 of the most recent tax table update:

  • Select the ‘Employees’ tab.
  • Choose the ‘Get Payroll Updates’. 
  • Next to the Payroll Update Info button, you’ll find the tax table version.

Let’s check to see if there are any errors or zero deductions for the Social Security and MD amounts on the employee’s paycheck, assuming you are using the correct version:

  • Navigate to the Reports menu.
  • Choose Employees & Payroll.
  • Select Payroll Detail Review.
  • If you want to run a specific report, select the ‘Customize Report’ tab. 
  • Select the Display tab, either type in the “From and To” dates or choose a ‘date range’ from a drop-down list. 
  • Pick the Payroll Item in the Filter section of the Filters tab. In the Payroll Item drop-down list,  choose multiple payroll items.
  • Choose the Social Security Company, Social Security Employee, Medicare Company, and Medicare Employee.
  • Click OK twice when finished. 

Verify the checks deductions on the report to ensure they are accurate. By multiplying the total wage base of each payroll item by the corresponding tax rate, you can obtain an accurate calculation. There is nothing more to do if the numbers are accurate.

There are two ways to fix the problem if QuickBooks over-withheld the Social Security and MD taxes. This is how:

Option 1: Add the taxes to your upcoming pay. A rate-based tax calculation feature in QuickBooks automatically subtracts overpaid taxes from your subsequent payroll run.

QuickBooks offers an accurate and effective automatic calculation feature for this. It will update the overpaid taxes to your upcoming payroll run for rate-based tax deductions. 

Option 2: You could make a liability adjustment to compensate for the extra payment.

  • You must first delete all the company files and the QuickBooks Desktop account.
  • On the toolbar, click the Windows icon.
  • Run a QuickBooks Desktop search.
  • Select ‘Run program as an administrator’ a right-clicking on the icon.
  • You must access the Help menu from the ‘Open screen’ of ‘No Company’ and choose the Update QuickBooks Desktop’ option.
  • Navigate to the Options tab. 
  • Choose Mark All, then click Save. 
  • You must click the Update Now button and then select the Reset Update checkbox.
  • Once you are prepared, click ‘Get Updates’.

If your employee’s payroll taxes are not deducted, you must check the order of the payroll items on the paycheck. You’ll be able to tell if the payroll item order is affecting the calculation. After all of this, you might include some additions and deductions in your calculation. You must include the payroll item after those items. 

Next, check to see if the payroll item is set to calculate quantity and hours. As a result, after a payroll item is configured to calculate based on quantity or hours, you will need to manually enter the quantity or number of hours in the Quantity column of the Preview Paycheck window. It will remain accurate using this strategy as well. It is advised that you adjust the payroll item’s calculation settings. How to do it is as follows: 

  • You must choose Lists and Payroll Item List from the top menu bar.
  • After that, you must right-click the payroll item you wish to modify and select “Edit Payroll Item.”
  • If the calculation is based on quantity, select Next. 
  • Then, click on Finish. 

Then, you need to see if the annual cap has been established or has already been reached. It might be a checkmark if a payroll item has consistently been correctly calculated in the past and stops computing on a paycheck. This is regarded as an annual limit checkbox with a default limit that the employee has reached. Please perform the actions listed below to verify this: 

  • Select Lists from the top menu bar. After that, go to the payroll item list.
  • The payroll item you want to change must be selected by right-clicking it and selecting Edit Payroll Item.
  • When the Limit Type screen appears, select Next.
  • Make sure the limit displayed in the bottom box is correct. If the mentioned limit is accurate, the calculation of the employee’s payroll item should end here. You must adjust the amount if the limit is inaccurate.
  • You should check to see if the right option was selected below the Limit Type.
  • Adjust the Limit Type selection or the Default Limit as necessary.
  • Then, click Finish.

Error: Only one employee’s Social Security and Medicare taxes were withheld incorrectly:

You can update your payroll tax table and QuickBooks Desktop to the most recent version available. Because the two products are outdated and your taxes may not be calculated correctly.

You can update your QuickBooks Desktop account manually by following these steps:

  • Close your QuickBooks Desktop account and company files.
  • Select Windows from the toolbar by clicking it.
  • Find ‘QuickBooks Desktop’. 
  • Run as administrator should be selected by right-clicking the icon.
  • Go to the Help menu in the No Company Open screen and choose Update QuickBooks Desktop.
  • Click on the Options tab.
  • Click Save after selecting Mark All.


This article contains all the details for QuickBooks Payroll Not Calculating Social Security issues. If you are still unable to fix the issue or are you searching for a qualified expert who can provide the best support for your issues? Our team of professionals and experts can correct any technical, functional, update, upgrade, or data migration errors you may be experiencing. Our team is available to help you around the clock.


1. Are unemployment taxes filed through QuickBooks payroll?

Navigate to ‘direct e-filing from QuickBooks Desktop. Create a state unemployment file in QuickBooks Desktop, then send it manually to the state (or send it online if necessary). Use QuickBooks Desktop to create paper copies of your unemployment forms, print them, and send them to the state. 

2. Why didn’t federal funds come out of my check?

If no federal income tax was deducted from your pay, the reason might be as obvious as the fact that you didn’t make enough money to warrant deducting any taxes. All of those factors will be taken into consideration when determining whether taxes should be deducted or withheld from your paycheck.

3. In QuickBooks, how do I change my payroll?

You can verify all the qualities of these financial items when the report opens. If changes need to be made, simply double-tap the specific employee for whom you want to make them. Navigate to the Payroll Info tab. Choose Taxes, then at least one tab each for Federal, State, and other fees.

4. How can I configure payroll taxes in QuickBooks?

Payroll software for QuickBooks (all versions) Choose Taxes from the Payroll Info tab. Select the State tab, then choose the appropriate work and Withholding States. You’ll be given the option to configure your state tax item. Pick Set up. 

5. How do you pay taxes using QuickBooks payroll?

Go to  Payroll Enhancement for QuickBooks Online Select Payroll Tax under Taxes. Decide on Pay Taxes. On the tax you want to pay, click Create Payment. Decide on E-pay.

6. How do I check Medicare and Social Security in QuickBooks?

Click the Filters tab after selecting the Customize Report option in the top left corner. Enter “Payroll Item” in the Search Filters box. Select Multiple payroll items by selecting the drop-down menu for All payroll items. Check Social Security and Medicare for the employee and the business by scrolling down. Press OK twice.

7. Why doesn’t QuickBooks calculate payroll taxes?

Payroll taxes may not be calculated for several reasons.

  • The employee’s most recent payroll gross salary is too low.
  • The salary limit is exceeded by the total annual salary.

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