I understand what's lacking in this process for you to claim employment allowances through QuickBooks Online, dpjyates. Let's ensure there is proper communication between HMRC and QuickBooks Online servers.
When processing payroll for your employees, it is necessary to submit Pay As You Earn (PAYE) data to HMRC. Activating the Real Time Information (RTI) reporting feature will ensure compliance. For guidance on enabling this option, please refer to the following article: Turn on RTI reporting to HMRC in QuickBooks Online Standard Payroll.
Once you have completed that, you should be able to submit Employment Payment Summary (EPS) and Full Payment Submission (FPS) to HMRC. Keep in mind, the steps required may differ based on your payroll subscription. Here are the relevant links for further guidance:
Submitting EPS
Submitting FPS
If you need additional assistance in settling your employment allowances, we'd recommend reaching out directly to the HMRC Support Team. They can give you the best options to address your concerns.
Additionally, feel free to post your questions in the Community or respond directly in this thread. Our team will be here to provide further assistance.