Open the employee in QuickBooks Online Payroll, edit their Deductions and contributions, and either delete the one-time deduction or change it so it no longer takes an amount. Check the next pay preview before you approve it.
This is general information, not professional advice.
Intuit does not publish a page titled for this exact situation, so the steps below combine what its Canadian help articles confirm with a few checks you should do yourself. Where something is not confirmed, it says so.
Option 1: remove the deduction from the employee
- Go to Payroll, then Employees, and select the employee.
- Under Deductions and contributions, select Edit.
- Select the trash icon next to the deduction, confirm Delete, then select Done.
Intuit lists these steps for deleting a deduction. Deleting it from the employee profile stops it from being applied to later pay runs. Do this only if you do not need the deduction to repeat in future.
Option 2: keep it, but stop it taking money
- Open the same Deductions and contributions section and select the pencil (edit) icon next to the deduction.
- Change the employee amount so it takes nothing, or set the pay-period method to None if the screen offers it.
- Save, then select Done.
Intuit says the pay-period amount can be set to None for contribution-only items that rely on an annual limit. Whether that option appears for an employee deduction depends on the item, so look at the screen rather than assuming.
What about the annual maximum?
Intuit advises adding an annual maximum to avoid over-deducting. If you set one and the employee has already reached it, QuickBooks should stop taking the deduction for the rest of the year. A deduction that was a single amount is a good fit for this: set the maximum equal to that amount.
Be careful at year end. Users on Intuit forums report that the annual maximum starts again in a new calendar year. If so, a deduction that was only meant to happen once could begin again in January. I could not confirm this in an official Intuit article, so do not rely on the maximum alone. Remove the deduction, or zero it out, once it has finished.
Checks before the next pay run
- Open the pay preview and look at the deduction line for that employee. It should show zero or not appear.
- Compare the deduction total on previous pay stubs with the amount you meant to take. If it was taken twice, fix it with a correcting entry rather than editing past records in a hurry.
- If you need the deduction later, add it again as a new item with a clear description that appears on the pay stub.
Making the item inactive
Intuit says an item can be made inactive when no employee is using it. Remove it from every employee first, then use View inactive items, choose the item, and select Make inactive. There is no list for deleting the item itself.
If it still comes through
If the deduction keeps appearing after these changes, contact QuickBooks Payroll support. Tell them the employee, the deduction name and the pay date where it reappeared. Keep before and after screenshots of the Deductions and contributions section.
Sources
- Intuit: Set up voluntary deductions in QuickBooks Payroll (Canada)
- Intuit: Set up and add deductions and contributions to an employee in QuickBooks Online Payroll
- Intuit Community: Payroll Deductions (user reports, not official)
Last checked: 18 October 2026