You will be notified by HMRC to request you register for Making Tax Digital. Once you register, any Return submitted from then on will have to be filed using MTD rules. Most companies are choosing to register only when they have submitted the last return they are able to using the existing rules.
With the above in mind, not all companies will have to submit using MTD straight away. Within CIA, you have the ability to submit using the existing VAT scheme or MTD. The default will be the existing VAT scheme.