I have just set up Quickbooks online payroll but employee auto enrollment contributions are not being treated as tax deductible in the NI EE calculation.
Thank you for dropping by here in the Community. I'm here to lend a hand with your concern about the auto-enrollment contributions in QuickBooks Online.
Can you share with me if this is the first period they supposed to have auto-enrollment contributions? If yes, you may need to consider checking the dates for their pay period to determine the staging date and the set up from the auto-enrollment section.
If you set up any postponement, it'll stop the system from taking contributions. If all fails after checking all the steps above, I recommend reaching out to our Support Specialists.
One of them will need to check this further through the system. You can follow these steps to reach them:
Log into your QuickBooks account.
Click the Help option in the upper-right corner.
Click Contact us.
Please know I'm always available here to help you with your payroll needs. The Community is here to ensure your success.