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.

Hi c-edwards,

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:

1. Log into your QuickBooks account.
2. Click the Help option in the upper-right corner.
3. 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.