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Set Up Pre-tax Deductions in QuickBooks Desktop & Online

Set Up Pre-tax Deductions in QuickBooks

If you give employees benefits, you probably have questions about how to properly deduct money from their paychecks to cover those benefits. What is withheld—pre-tax or post-tax—from the premiums and contributions? Do you have the option to choose how much to withhold? According to the benefit, obviously. The distinction between pre-tax and post-tax deductions is thus important to understand.

Payroll now involves more than just paycheques. Employee expenses like health insurance, retirement contributions, uniforms, tools, and dues can come up from time to time. Perhaps you gave your employees a paycheck advance that they need to repay. These advantages or deductions can be configured in QuickBooks Payroll. Each pay period will be deducted from your employee’s pay. The cost of things like employer-provided employee benefits or general deductions like a charitable contribution is deducted from an employee’s net pay as part of voluntary payroll deductions. Pre-tax deductions must be made from taxable wage items, please note. They won’t take anything away from a reimbursement.

Before you deduct taxes, you will deduct pre-tax deductions from an employee’s pay. Pre-tax deductions lower the amount of income on which the employee must pay taxes. After deducting taxes from an employee’s paycheck, post-tax deductions will be withheld. No impact is made on an employee’s taxable income by post-tax deductions. Pre-tax and post-tax 401(k) plans are two examples of benefits that can be either way taxed. The kind of deduction you must typically make is already specified in the benefit’s policy. If a benefit has pre-tax vs. post-tax deductions, you or the employee may occasionally have a choice.

Pre-tax deductions lower an employee’s taxable income, which lowers their tax liability. Additionally, they might owe less FICA tax, which covers Medicare and Social Security. Employer-paid taxes like the Federal Unemployment Tax (FUTA), FICA, and SUI are reduced by pre-tax deductions. 

The voluntary payroll deductions in QuickBooks Online (QBO) cover both pre-tax and post-tax premiums for health, dental, and vision insurance. Garnishments, on the other hand, are not voluntarily made deductions. For the deduction item to be available when adding a deduction to the rest of your employees, you’ll need to ensure that you’ve set up a new deduction for your employees.

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Mandatory Deductions

These sums must be withheld by employers and paid to the appropriate authorities as required by law.

Payroll Tax Deductions:

The income tax deduction is the most glaring example of these types of necessary deductions. When a worker earns more than the ATO-set threshold, income tax will be withheld. The amount over the threshold will be taxed; however, an employee may decide not to claim the tax-free threshold in which case taxes will be assessed on the entire amount. Their TFN (Tax File Number) declaration information will reveal whether they are claiming the tax-free threshold.

Payroll deductions for debt repayment under the Higher Education Loan Program (HELP), VET Student Loan (VSL), Financial Supplement (FS), Student Start-Up Loan (SSL), or Trade Support Loan are another category that is required by law (TSL). Before mandatory repayments are required, thresholds apply. Typically, based on data from the TFN declaration, this additional deduction is incorporated into the PAYG withholding amount.

Your taxable income is subject to the Medicare levy. This is typically covered by the PAYG withholding amount taken from the employee’s gross pay.

Pre-Tax Deductions

Payroll taxes should be subtracted prior to pre-tax benefit deductions from employee compensation. Workplace giving deductions allow employees to regularly give to charities or other organizations. Pre-tax or post-tax options are available. If they opt to give pre-tax, the amount decreases the value of the gross wages used to determine how much PAYG withholding tax will be deducted from their donations. They can choose to deduct this donation from their personal tax return if they make it as a post-tax donation because doing so will not affect their taxable income.

  • Reduced tax obligations for both you and the employee are a benefit of pre-tax deductions. When using the benefits, the employee might eventually owe taxes. As an illustration, a retired employee who withdraws funds from a 401(k) plan before taxes will be taxed.
  • Aside from that, not all pre-tax benefits are exempt from federal tax withholdings in full. The federal income tax withholding requirement does not apply to adoption assistance, for instance. But neither the Social Security and Medicare taxes nor the FUTA tax are exempt from adoption assistance.
  • The sacrifice of pay in order to contribute to their compliant superannuation fund, employees who participate in superannuation must sacrifice a pre-tax amount or percentage of their pay. This sum is a reportable employer super contribution (RESC) on their annual income summary, and it has no bearing on the calculations used by the employer to determine how much superannuation to pay.

Post-Tax Deductions:

  • Fees paid by employees to join a union or professional organization are known as union or professional association fees.
  • Child support is deducted from employees’ paychecks in order to cover payments made to Services Australia. When child support is deducted, there is a portion of the employee’s pay that is a Protected Earnings Amount (PEA) and is not subject to withholding.

Pre-Tax Deductions vs. Post-Tax Deductions

Before taxes are withheld, pre-tax deductions are subtracted from an employee’s gross pay. Pre-tax deductions lower an employee’s taxable income, which is the amount used to determine their tax. Salary sacrifice options like laptop computers, cars, workplace donations, and superannuation are typical pre-tax deductions.

Post-tax deductions, on the other hand, are subtracted from an employee’s net pay following the withholding of all applicable taxes. Union/professional association dues, workplace donations, and child support are examples of common post-tax deductions. Except for wage garnishments, employees are free to opt out of any post-tax deductions.

Contribution vs. Deduction

A deduction is a sum of money that an employee pays and has taken out of each paycheck. Employer contributions frequently count as extra compensation or wages.

For instance, a health insurance plan may require contributions from both the employer and the employee. A deduction is used to describe the employee-paid portion. A contribution is what the employer contributes.

Examples of frequent pre-tax deductions are:

  • 401(k) plans are some retirement programs.
  • medical protection
  • HSAs, FSAs, and Life Insurance
  • Transport-related initiatives
  • According to the policies your company has established, you might need to withhold some of these deductions after taxes.

Follow these steps to accomplish this: 

  • Choose your employees. 
  • Pick the name of the worker.
  • Near Pay, click Edit.
  • Choose + Add a new deduction or + Add deductions from section 5’s drop-down menu.
  • Select New Deduction/contribution under the Deductions/Contributions drop-down menu.
  • Select a deduction type and type using the tiny arrow icon.
  • The name of the service provider should be entered (appears on a paycheck).
  • Enter the dollar amount or percentage of gross pay by selecting it from the Amount per pay period icon. The Company-paid Contribution should be treated in the same way, as appropriate.
  • Click Done after selecting OK.

The pre-tax insurance item’s tax tracking type needs to be updated. The desired box receives the reported amounts in this manner. I’m here to walk you through the entire process.

  • Activate the QuickBooks Desktop file.
  • Select Payroll Item List from the Lists menu.
  • Find the item and double-click it to launch the Edit payroll item window.
  • Press Next up until you reach the Tax tracking type page.

You must delete your payroll and start over after updating the item. This assists you in updating the amounts to the appropriate box or code. 

Void or Delete employee Paychecks:

Find out how and when to fix an employee’s paycheck. After a payroll check or direct deposit payment has been submitted, you can cancel, delete, or void it.

Want to modify a paycheck, stop a direct deposit, or stop your payroll run? Apply the advice in this article if you:

  • made a copy of the paycheck
  • entered incorrect information on a paycheck (such as hours, deductions, additions, or paycheck or pay period dates)
  • wrong gross or net pay
  • incorrect work sites

Should you Delete or void a paycheck?

QuickBooks may let you delete or void a paycheck depending on your processing speed and payroll provider.

  • To delete a paycheck:
    As a result, the transaction is dropped from your payroll. If the paycheck hasn’t been delivered to the payroll service, use QuickBooks Desktop Payroll to process it. If the paycheck hasn’t been processed yet, you can do this using QuickBooks Online Payroll.
  • Void a check:
    This updates the dollar amount of the check to zero in your paycheck records. To balance your books, adjustments might be necessary. This doesn’t prevent a direct deposit from going through and doesn’t give you your money back.
  • Void or Delete paychecks:
    For information on direct deposit processing deadlines and how to stop receiving paychecks via direct deposit, select your payroll service from the list below:

QuickBooks Payroll Online:

Try to void or delete the paycheck

The paycheck might be able to be deleted or voided. 

  • Navigate to Employees after Payroll.
  • Decide on the Paycheck list.
  • Select Delete or Void, then choose the paycheck(s) you want to delete or void.
  • Choose Yes.

QuickBooks Payroll Desktop: 

Step 1: Try to delete the paycheck 

You can delete the paycheck if you haven’t sent it to the payroll service.

  • Select Use Register from the Banking menu.
  • Select the question check, then open it.
  • Select Delete at the top of the paycheck.
  • Enter OK in the pop-up box.

Step 2: If you can’t delete the paycheck

You can void the paycheck if payroll is sent to QuickBooks. Payroll taxes and direct deposit may still be deducted from your bank account, depending on how quickly your processing is completed.

Payroll should be voided and sent to the employee via direct deposit: 

Step 1: Cancel direct deposit paychecks

  • Choose Edit/Void Paychecks from the Employees menu.
  • Change the Show paychecks through/from dates to the date of the wages you need to void, then press Tab on your keyboard.
  • Choose Void under the check-in question.
  • Type YES and choose Void in the pop-up box.
  • To accept the terms and conditions of nullifying the paycheck, check the appropriate box.
  • To include all checks that need to be voided, repeat steps 1 through 5 as necessary.

Step 2: Send the canceled checks

  • Choose to Send Payroll Data from the Employees menu after choosing Employees.
  • Select Send. Although you won’t see any direct deposit checks to send, this informs our system to stop sending out paychecks. 
  • After entering your payroll PIN, click OK. 

Create and manage your payroll:

Learn how to create direct deposit or paper paychecks and send them to QuickBooks payroll for processing.

We’ll walk you through the process of creating your paychecks in QuickBooks Online Payroll or QuickBooks Desktop Payroll and sending them to us for processing payroll taxes and direct deposits. 

Step 1: Give your employees a pay schedule.

Payroll management can be made more effective by using pay schedules. Create a payroll schedule for your employees if you haven’t already.

Step 2: Prepare your payroll and send it. 

You must then prepare your paper paychecks or direct deposits and send them to us for processing. You can create a scheduled payroll or an unscheduled payroll if you’ve set up a payroll schedule.

  • Paychecks you regularly give to your employees are known as scheduled payroll. These paychecks can be supplemented with bonuses or other compensation.
  • Unscheduled payroll: You might need to pay your employees’ bonuses, commissions, a parting gift, or report fringe benefits outside of your typical payroll cycle.

AFLAC is add-on insurance.

Let’s create the item first. This is how:

  • To access the Payroll Item List, first, click Lists.
  • When you click Payroll Item, choose New.
  • Click Next after choosing Custom Setup.
  • Click Next after selecting Deduction.
  • Click Next after entering the desired name.
  • Click Next after entering the agency’s name and choosing the liability account.
  • Click Next after selecting the tax tracking type.
  • On the Taxes page, select Next.
  • On the Calculate based on quantity page, choose Neither, then click Next.
  • Next, select Gross Pay, and then click.
  • Click Finish after entering the rate and limit.

Let’s add it to the employee profile next. This will ensure that the item appears when you create the paycheck. As follows: 

  • To access the employee center, first, click Employees.
  • Open the employee’s profile by clicking twice on their name.
  • the Payroll Info tab.
  • The AFLAC item should be added under Additions, Deductions, and Company Contributions.
  • Specify the amount.
  • Choose OK.

Note: The pre-tax insurance item’s tax tracking type needs to be updated. The desired box receives the reported amounts in this manner. I’m here to walk you through the entire process.

  • Activate the QuickBooks Desktop file.
  • Select Payroll Item List from the Lists menu.
  • Find the item and double-click it to launch the Edit payroll item window.
  • Press Next up until you reach the Tax tracking type page.

QuickBooks Online offers the option to create pretax deduction types. 

Steps to create pre-tax deduction types: 

  1. Visit the employee’s profile and choose the worker.
  2. Select the + Add deduction link under Section 5 and then click.
  3. Click on these deductions from the drop-down menu:
  • Contribution, garnishment, or deduction: Deduction/contribution
  • Health Insurance Type of Deduction/Contribution
  • Healthcare insurance.
  1. Include the details of the providers and the sums for the Employee and Company-paid fields.
  2. Select Pre-Tax Insurance Premium, then hit OK.

With Standard payroll, adding a deduction in QuickBooks desktop:

If you haven’t yet issued the paycheck, you can delete or void it after updating your tax table if you’re still in the payroll creation phase.

Additionally, make sure the deduction item has been added to the employee’s profile. As follows:

  • Then select the Employees menu.
  • Open the relevant employee’s profile by selecting Employee Center.
  • Enter the 401(K) deduction item under Additions, Deductions, and Company Contributions in the Payroll Info tab.
  • When finished, click OK.

It is necessary to establish a pre-tax fringe benefit deduction (which lowers taxable income) for employee commuter benefits. Although prohibited by SF law, why is this supported by QBO?

You cannot use a particular payroll item to set up the fringe benefit deduction (Commuter Benefits). The Deduction/Contribution option, however, enables you to create a pre-tax item. 

Check out the following articles for a summary of the deductions and contributions offered in the online version. The steps to assign the payroll item to your employees are also included, along with comprehensive instructions on how to enter it.

Learn how to add deductions that your employee must make each pay period in QuickBooks Online Payroll and QuickBooks Desktop Payroll. You can set them up, modify them, or remove them.

Payroll now encompasses more than just paychecks. Workers occasionally have health insurance, retirement contributions, uniforms, tools, or dues to cover. Perhaps you gave your employees a pay advance that they must now repay.

Configure a new deduction item.

You can set up items for pre-tax or post-tax deductions in QuickBooks Payroll. Speak with your plan administrator or a CPA if you are unsure of how the deduction is taxed. Set up general deductions for things like uniforms, tools, commuter benefits, or other expenses by following the instructions below: 

QuickBooks Payroll Online: 

  • Select Employees, then Payroll.
  • Choose an employee.
  • To start or edit a deduction or contribution, choose Start or Edit.
  • Select + Add deduction/contribution from the Deduction/contribution dropdown menu.
  • Choose a Type and Deduction/contribution type. Choose Vision Insurance if you need to set up a pre-tax item that isn’t listed, such as commuter benefits, AFLAC, etc. Select Pre-tax insurance premium after Step 7.
  • Describe the situation. This is the name of the deduction or plan. is written on paychecks.
  • Choose whether a flat amount or a percentage of your gross pay should be used to calculate the deduction. Enter the sum or percentage after that.
  • Pick Save, then click Done.

QuickBooks Payroll Desktop: 

Step 1: Create the deduction item.

  • Select Lists, then Payroll Item List.
  • Select New from the Payroll Item dropdown menu.
  • Select Custom Setup, then click Next.
  • Select Deduction and then press Next.
  • Choose Next after entering the deduction’s name.
  • If applicable, choose (or add) the name of the plan administrator and the account number. then click Next.
  • Choose the appropriate Tax tracking type. If the deduction is post-tax, choose None.
  • Three times, select Next.
  • In the Gross vs. Net window, choose Net Pay for the None tax tracking type, then click Next.
  • Unless these apply to all of your employees, leave the default rate and limit fields empty. When the item is added to the employee profile, you will add the rate and cap.
  • Select Finish.

Step 2: Include the item in the employee profile.

  • Select Employee Centre, then Employees.
  • Pick an employee.
  • Decide on Payroll Info.
  • The deduction item should be added to Additions, Deductions, and Company Contributions.
  • Enter the amount for each billing cycle and, if necessary, a limit.
  • Click OK.

Create a new line item for employee deductions: 

You can create pre-tax or post-tax deduction items in QuickBooks Payroll. Speak with your plan administrator or an accountant if you have any questions about how the deduction is taxed. The procedures listed below can be used to set up general deductions for things like uniforms, equipment, commuter benefits, and miscellaneous.

Add a line item for employee deductions. When adding a deduction to the other employees, you can choose this deduction item once it has been set up for one employee.

QuickBooks Online Payroll:

  • Select Employees, then Payroll.
  • Choose an employee.
  • To start or edit a deduction or contribution, choose Start or Edit.
  • Select + Add contribution/deduction.
  • Choose Contribution or Deduction.
  • Describe the situation. This is the name of the deduction or plan. shows up on pay stubs.
  • Choose a Deduction/contribution type and Type to add a new deduction.
  • Choose whether a flat amount or a percentage of your gross pay should be used to calculate the deduction. Enter the sum or percentage after that. Apply the same principle to any Company-paid Contribution.
  • Pick Save, then click Done.

Assigning a deduction item to employees:

Set up deductions that can be automatically paid into a bank account or super fund, as well as set to automatically expire after a specific date or time, to simplify payroll.

Establishing your deduction categories is the first step in using deductions. This enables you to create specialized deduction categories that can be adjusted to meet the demands of your company. By assigning it to other employees, you can add the same deduction that you’ve set up for one employee.

Setting up deduction categories:

  • From the left-side menu, choose Employees.
  • Deduction Categories can be found by selecting the Payroll Settings tab (located under Pay Run Settings).
  • Choose Add, then type a name for the deduction.
  • Fill out the Deduction Type and any additional pertinent fields, then click Save.

QuickBooks Online Payroll:

  • Select Employees from Payroll by going there.
  • Choose the employee.
  • Choose + Add a new deduction or + Add deductions in section 6 Deductions/contributions.
  • From the dropdown menu, choose Add deductions/contributions.
  • Choose the existing deduction you want to apply for your employee from the Deduction/contribution type.
  • Choose whether you want the deduction to be calculated as a Flat Amount or as a Percentage of Gross Pay. then type the sum or percentage.
  • Choose Save, then click Done.

Edit a payroll deduction item

You must follow the procedures for your product if you want to alter the employee’s deduction information, including the amount, percentage, or description.

  • Payroll through QuickBooks Online
  • Access Employees after Payroll.
  • Pick a worker for the job.
  • Choosing Start or Edit from Deductions & contributions.
  • When a deduction is displayed, click Edit.
  • When necessary, edit the information.
  • Choose Save, then Done.

Delete a payroll deduction item

If you want to remove a payroll deduction item, follow the instructions for your product.

QuickBooks Online Payroll:

A deduction made to your employee may be removed. There is no “list” to eliminate deduction items from payroll.

  • Select Employees, then Payroll.
  • Choose an employee.
  • Choose Start or Edit under Deductions & contributions.
  • Next to the deduction you want to delete, select the trash can icon.
  • Then click Done after selecting Delete.

Checking the status of a deduction:

When you go back to Pay Run inclusions after setting up your deductions, you can view a summary of the deductions, which will include:

  • The quantity or time frame for the deduction’s termination
  • The date on which the deductions began
  • Regardless of whether the deduction has ended
  • For expiries with a value, the most recent sum that has been paid
  • The method of payment selected for this deduction.

Manage payroll items for your insurance benefit plan by setting them up:

To properly track and tax your insurance benefit plan, learn how to set up and manage payroll items for it in QuickBooks Online Payroll and QuickBooks Desktop Payroll. You might need to set up items in QuickBooks to track if your company offers insurance benefits.

You can add, edit, and track your insurance benefit plan in QuickBooks by following these steps:

Step 1: Select the health benefits to establish

  • Section 125 programs (Cafeteria benefit plans)
  • HSA Programs
  • Accounts with variable expenses (FSA)

Step 2: Create a payroll item for health, vision, or dental insurance.

You can add a payroll item for medical, vision, or dental insurance by following the instructions below once you have the specifics of the insurance benefits from your provider.

QuickBooks Online Payroll:

Note: Use the vision insurance line item for any other pre-tax insurance that QuickBooks does not already list.

  • Navigate to Employees after Payroll.
  • Pick an employee.
  • Select Start or Edit under Deductions & contributions.
  • To add a deduction or contribution, select +.
  • Pick one of the options from the drop-down menu:
    • Deduction/contribution: Include a deduction or contribution
    • Type of contribution or deduction: Health coverage
    • Type: Decide between medical, vision, and dental insurance.
  • The provider’s name should be entered in the Description (appears on paycheck) field.
  • After choosing a Flat Amount or Percentage of Gross Pay, enter the Amount or Percentage for each Paycheck.
  • Pick either Taxable or Pre-tax insurance premiums.
  • If your employer matches your contribution, be sure to include a dollar amount or percentage with each paycheck.
  • Once finished, choose Save and then Done.

Step 3: Make sure the items are on your employees’ paychecks

These benefits should be reflected in each paycheck you send to your staff members.

Edit or remove an insurance item:

Following are instructions on how to modify or remove an insurance item:

  • Payroll through QuickBooks Online
  • Access Employees after Payroll.
  • Pick a worker for the job.
  • Choosing Start or Edit from Deductions & contributions.
  • The contribution you want to change or remove can be selected by clicking Edit next to it or by clicking the Trash icon.
  • Choose Save, followed by Done.

Track insurance benefit plan contribution:

Learn how to run payroll reports in QuickBooks Online Payroll and QuickBooks Desktop Payroll if you need to run a report for the insurance benefit plans.


The list of payroll deductions that both employees and employers should be aware of that is provided here is by no means comprehensive as it only includes the most typical types. Payroll deductions can be required, optional, pre-tax, or post-tax. You can better understand where a portion of your pay goes each pay period by being aware of the various types of deductions.

Frequently Asked Questions

Q1. How do I configure tax deductions in QuickBooks?

  1. Go to QuickBooks Home and select Lists > Payroll Item List. 
  2. A list of payroll items can be found on the following screen. Choose the deduction you want to configure > Double-click that deduction. 
  3. Type in the name of the deduction that will appear on your paycheck and payroll reports. 
  4. Select Next.

Q2. How do I configure QuickBooks Desktop’s EZ setup?

Click Lists > Payroll Item List from the QuickBooks Desktop menus at the top of the screen. Click Payroll Item and then click New in the lower left corner of the Payroll Item List. Click Next after selecting EZ Setup.

Q3. In QuickBooks, how do I create a tax tracking type?

The QuickBooks Desktop file is now open. Payroll Item List can be found by selecting the Lists menu. To open the Edit payroll item window, locate the item and double-click its name. Once you’re directed to the Tax tracking type page, click Next.

Q5. How do I MAP payroll deductions in online QuickBooks?

  1. Access the Gear icon.
  2. From the Your Company section, choose Payroll Settings.
  3. Go to Preferences and select Accounting.
  4. Choosing Edit will take you to the Paycheck and payroll tax payments section.
  5. Pick the account you created in your Chart of Accounts from the drop-down menu for the bank account (COA).
  6. To continue, click. Then, press Finish.

Q6. How can I create a pre-tax deduction in QuickBooks desktop?

  1. Navigate to the employee profile.
  2. Choose the employee, navigate to section 5, and click the + Add Deduction link.
  3. The following choices from the drop-down menu:…
  4. Fill in the Employer and Amounts Paid by Company fields with the appropriate information.
  5. Choose the Pre-Tax Insurance Premium option.
  6. Press OK.

Q7. How do I classify 401k contributions in QuickBooks online?

  1. Select Payroll Settings by clicking the gear icon in the top-right corner.
  2. Select Deductions / Contributions under Payroll.
  3. Choose Add a New Deduction/Contribution.
  4. Choose Retirement Plans under Category.
  5. Choose the appropriate retirement plan under Type.
  6. Type in the provider or plan’s name.
  7. Hit Ok.

Q8. What are the steps for entering employee contributions into QuickBooks?

  1. Select Employees after clicking Payroll in the left menu.
  2. Pick out each worker on the list.
  3. Select Pay by clicking the pencil icon next to it in the employee’s profile.
  4. Is this employee subject to any deductions?
  5. Complete the required fields and the contribution that the company will pay.
  6. Click OK and then Done.

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