We were not made aware that taxable benefits were being provided to an an employee on June 1st, so it was not included on the last 3 pay cheques. Can these benefits be added retroactively so that applicable taxes are paid & shown on the employee's T

Welcome to Community!  QuickBooks Online Payroll enables you to set up employee deductions and contributions seamlessly.  It's essential that all payroll deductions and contributions are set up correctly, to ensure accurate calculations when submitting payroll.  I would be glad to assist!

In your situation, you'll want to make sure the employee is set up with the required deductions and contributions.  These can easily be entered and applied to the employee by following the steps here.  Once they've been added to the employee profile, you can run an unscheduled payroll for the amount owing, or make the necessary adjustments on your next pay run.  However, I do recommend speaking with an accounting professional for their expertise and best course of action.  If you don't have an accountant, we can help you locate a ProAdvisor in your local area.

Should you require additional assistance, please don't hesitate to contact us outside of this forum. It would be our pleasure to work with you in real time, and ensure you're able to accomplish your QuickBooks goals without delay!

Feel free to reach out again, if you have any other questions. We would be happy to help!