Please skip to Step 2 if you have already amended your VAT settings in Clear Books.

Step 1.

Navigate to Tax > VAT > MTD onboarding > Click on 1. Update your Clear Books VAT settings > Click Update Settings. The system will then automatically toggle on the Online VAT Filing and MTD VAT Submission features

Once this has been completed, a green tick will appear beside step 1 to confirm this.

Step 2.

Click on 2. Register for the MTD VAT pilot > Click Manage Agent services account. You must create an Agent Services account to access the new HMRC services, in this case, MTD VAT submissions which will include two sub-steps. If you already have an existing Agent Services account, please proceed to Step 3.


This will direct you to the Government Gateway page or alternatively, click here. You will then be prompted to create a Government Gateway account where you will have to choose the relevant Government Gateway account type and input your preferred registration credentials. Subsequently, HMRC may require your Self Assessment unique tax reference (UTR) or Corporation Tax reference number and Postcode to identify your business.

As soon as this has been completed, HMRC will then automatically generate a unique Government Gateway User ID and send a copy of this to the registered email address. 


You must then proceed to create an Agent Services account by following this link > Log in using the User ID and password obtained from the step above > Complete the steps to create your Agent Services Account. Note down your Agent Services Account number to use later. Keep this somewhere safe because it cannot be recovered if you lose it! This is sometimes also called an Agent Reference Number (ARN).

Step 3.

Follow the instructions on-screen to create a VAT service in your Agent Services Account.

Step 4.

Access the following link to log in to your Agent Services account > Navigate to the link; “Allow this account to access existing client relationships” located under the “Services you might need” section > Log in using the User ID and Password for the old Government Gateway ID you use to access the clients you wish to link > Then enter your Agent Services Account number and business tax reference (sometimes called a “Self Assessment UTR” or “Corporation Tax reference”) and follow the steps to link your clients.

Once completed, you will see a success screen indicating that you have connected the Government Gateway ID. Repeat for any other Government Gateway IDs for other clients you wish to link. This will then be reflected in Clear Books where a green tick will appear beside step 2 to confirm this.

Step 5.

During the MTD VAT pilot, which started in April 2018 and is expected to end in July 2018, the next step is to opt-in your client for MTD VAT. In order to do this, you can expect to receive an email from HMRC containing instructions and a link for you to opt-in your client for MTD VAT.

Once triggered, this is a batch process which runs overnight and may take up to two nights. HMRC will email you once this has successfully completed.

Step 6.

You must then head back to Clear Books MTD onboarding and click on 3. Authorise Clear Books software to submit VAT returns to HMRC > Click Authorise > You will then be redirected to the Government Services website, where you will have to click Continue > Input your credentials and click Sign In > Then click Grant Authority in order to authorise Clear Books.

Again, a green tick will appear beside step 3 to confirm this.

Step 7.

Click 4. Submit your MTD compliant VAT return > Click Prepare MTD VAT return, which will redirect you to the VAT return page on Clear Books where you can select the obligation dates provided by HMRC and search for the invoices/ bills within this period and create the return, then submit this directly to HMRC.

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