Please refer to our FAQ number 4700 'how to set up and claim the Employment Allowance' and double check that you have followed all the instructions on how to set up the Employer Allowance Claim and how to inform HMRC.
Please note, in step 1 when indicating the claim in the Chart of Setup section, do not enter any figures for the Employer Allowance you have claimed back to date in this tax year (unless appropriate). The £3000 claim has already been entered for you.
Road Map - Edit Employment Allowance Indicator Setup
Employer/Setup -> Chart of Setup -> Payrun Customisation -> Employment Allowance Indicator Link -> Edit button -> Select "Yes" -> Click on Save.
( 'Employer/Setup' is the button positioned in the tasking zone menu at the top. It is the first button from the left)
Also, check to see that you have successfully e-filed the EPS telling HMRC that you are claiming the £3000. Check E-filing Status to confirm that it has been sent successfully and click on the E-filing Details to check that the Employment Allowance Indicator is set to 'Yes'.
Road Map - To Find out the E-Filing Status and check the details
E-Filing RTI -> E-filing Status -> EPS (Employer Payment Summary)
( 'E-Filing RTI' is the button positioned in the tasking zone menu at the top. It is the third button from the left)