You can only delete a VAT Return when it is a draft (not submitted to HMRC) or when your VAT submission has failed.
Submitted VAT return manually by mistake
This can happen if you are registered for Making TAX Digital (MTD) and selected Submit to HMRC by other means by mistake.
To resolve this you will need to re-submit the VAT return. Read How to re-submit a manual VAT return with MTD.
Delete a draft VAT Return
- From More, select VAT Returns.
- Select Delete next to the return you want to delete.
- When prompted, select Yes.