In a bid to improve Making Tax Digital for VAT compliance, HMRC will remove the ability to submit online VAT returns for some businesses that should have signed up for it.

From April 2019, most VAT registered businesses with a turnover above the VAT registration threshold were required to join Making Tax Digital for VAT or Making VAT Digital (MVD). 

If this approach is successful in improving MVD compliance, HMRC may use it more widely.

HMRC can charge a Penalty of up to £400 where businesses that are required to report via MTD file a VAT return by non-MTD means.

Useful guides on this topic

Making Tax Digital: VAT (subscriber guide)
What is Making Tax Digital (MTD) for VAT? What is VAT 'functional compatible' software? What do you need to report their VAT? Are there penalties for making mistakes?  

Penalties (VAT)
When do penalties apply for VAT? What penalties are charged and how can they be mitigated?

Registering for VAT
When should a business register for and charge VAT? What are the VAT registration limits and VAT rules after Brexit? What penalties might HMRC issue for late notification of registration?

Source

ICAEW


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