MTT55140 - Administration: Compliance: Compliance checks: Taxpayer amendments
Source: gov.uk (2025-08-05)


If a filing member amends the self-assessment return while a compliance check is in progress, the amendment does not restrict the scope of the compliance check but may be considered together with any matters arising in the compliance check.

Any potential changes to the tax liability as a result of the amendment only become effective once the compliance check is closed. See MTT55170 (https://www.gov.uk/hmrc-internal-manuals/multinational-top-up-tax-and-domestic-top-up-tax/mtt55170) for guidance on closure notices.

A compliance check does not extend the time limits for making an amendment. If the time limit for amending the return has expired, the filing member cannot amend the return. See MTT53000 for guidance on amendments to the self-assessment return.

If the filing member is within time to amend its return, HMRC may take the amendment into account as part of the compliance check before issuing a closure notice, even if this means prolonging the compliance check to deal with any new points raised.

This is set out in paragraph 20, Schedule 14 to Finance (No.2) Act 2023.

Effect of the amendment

An amendment will not take effect, insofar as the amendment affects the amount stated in the group’s self-assessment of the amount of tax payable, until:
- HMRC issues a final closure notice to complete the compliance check, and that notice specifies whether a deferred amendment is to take effect, and to what extent it is to take effect, or
- HMRC gives a partial closure notice which states that the amendment is to take effect, and that notice relates to a matter to which the amendment also relates or which is affected by the amendment.
If the conclusions in the final closure notice state that either:
- the amendment was not considered in the compliance check, or
- no amendment of the return is required arising from the compliance check,
then the amendment takes effect on the issue of the closure notice.

Otherwise, the amendment takes effect as part of the amendments made by the closure notice.

Amendment anticipating conclusions in a closure notice

As a result of negotiations leading up to the close of a compliance check, HMRC may receive a revised return from the filing member that fully and accurately anticipates the conclusions of the check before they are stated in a closure notice. The revised return may be submitted within the applicable time limits so that it is a valid amendment.

HMRC cannot conclude a compliance check into a group’s return by just accepting the revised return, even if the figures subsequently stated in the closure notice will be identical to those in the revised return. To complete the compliance check, HMRC must issue a closure notice.

The amendment will be deferred due to the ongoing compliance check and will take effect in accordance with the closure notice, as above.

Repayment during an ongoing compliance check

If the filing member of a group is within the time limit to amend its return during a compliance check, then an amendment which gives rise to a repayment does not restrict the scope of the compliance check but may be considered together with any matters arising in the compliance check.

Provided HMRC is satisfied that any such claim meets the requirements of the legislation, HMRC will follow the relevant procedures with respect to issuing a repayment.