Short answer
The VAT control balance and the current return are related but not identical measures. The control can include brought-forward amounts, prior-period liabilities or payments, while the return contains the VAT activity assigned to that filing period.
What to check first
Why this happens
The balance sheet control answers “what is still owed to or by HMRC?” while a VAT return answers “what VAT is reportable for this period?”. Payments, opening liabilities, prior filings and scheme-specific adjustments can make those amounts different.
Steps to resolve it
- Reconcile the opening VAT control to the agreed migration position.
- Review submitted returns and their filing evidence.
- Trace HMRC payments/refunds through the VAT control.
- Review the open return detail and any late-item carry forward.
- Investigate specific differences rather than posting a journal just to make the two totals equal.
What to avoid
Frequently asked questions
Should the VAT control always equal Box 5?
No. Box 5 is the net amount for one VAT return. The VAT control can also contain prior balances, payments/refunds and other timing items.
What should I do with an opening VAT liability?
Bring the agreed amount into the opening VAT control rather than recreating historic VAT returns that were filed before Balansix.
Does Flat Rate VAT change the control reconciliation?
Yes. Balansix distinguishes transaction-level source VAT from the FRS liability so the control reflects the scheme outcome rather than simply adding input and output VAT in the standard way.