In line with MTD, HMRC has introduced a brand new points-based penalty system for late submissions and penalties, aimed at encouraging compliance while offering a fairer approach than traditional automatic fines.
This new system is already in place for VAT returns and will come into force from April 2026 for MTD ITSA.
Late Submission Penalties:
Under the new rules, every missed submission deadline earns you one penalty point.
This includes:
- Quarterly MTD submissions for income tax or VAT
- Annual VAT returns
- Other scheduled digital submissions under MTD
Once a penalty threshold is reach, a £200 financial penalty is triggered. Thresholds vary based on the submission frequency:
| Submission Frequency |
Penalty Threshold |
| Annual |
2 points |
| Quarterly |
4 points |
| Monthly |
5 points |
Each type of submission is tracked separately. For example, if you have two businesses submitting quarterly returns, HMRC tracks points for each business independently.
How to Remove Points
Points expire after 24 months, but only if:
- You have brought all outstanding returns up to date;
- You complete a compliance period without further infractions:
- 24 months for annual submissions
- 12 months for quarterly
- 6 months for monthly
This encourages consistent, on-time filing.
Late Payment Penalties:
The new late payment penalties are time-sensitive and based on how quickly you settle your tax bill after the due date:
| Days After Due Date |
Penalty |
| 0 - 15 days |
No penalty if paid or Time to Pay agreed |
| 16 - 30 days |
2% of outstanding tax |
| 31+ days |
Additional 2% (totalling 4%) |
| After 31 days |
Daily penalties: 4% per annum on outstanding amount |
However, there is a first-year grace period for late payment penalties to adjust to the new regime. HMRC will allow up to 30 days for payment or a Time to Pay agreement before charging the first 2% penalty.