Help guide series for our Basic Accounting product

Connecting Clear Books to HMRC

HMRC requires digital records and quarterly updates for each distinct income source (e.g., self-employment, UK property, and foreign property are all treated separately). During this one-off setup, you will link your Clear Books business to a single HMRC income source.

• Hover over Tax in the top menu bar and select MTD for Income Tax - Setup.
• If you are not yet signed up for MTD, follow the provided link to HMRC. If you are already signed up, enter your National Insurance number and click Update.
• Click Authorise Clear Books to be directed to the HMRC portal. Log in with your Government Gateway ID and password to grant access.
• Once authorised, Clear Books will display your HMRC income sources. Select the one you want to link to this specific Clear Books account.

(Note: You only need to authorise Clear Books once. This is saved to your user ID, so you will not need to re-authorise for future businesses or tax returns.)

Your Submission Schedule

Once connected, your submission overview page will track your upcoming update periods and deadlines.

The standard quarterly end dates are the 5th of July, October, January, and April. You can optionally switch to calendar periods in your settings, which shifts the end dates to the last day of the corresponding months.

Submitting Quarterly Updates

Your dashboard will automatically notify you when a quarterly update is due.

• Click the dashboard notification to view your submission summary.
• Click into any category to review the specific digital records making up your totals.
• Click Submit. Clear Books will send the summary to HMRC, and the quarter will be marked as 'Fulfilled' upon receipt.

Tracking Status & Troubleshooting

You can check your current MTD obligations at any time by hovering over Tax in the top menu and clicking MTD for Income Tax.

• Successful Updates: A green tick alongside a ‘Fulfilled’ status means HMRC has received your data and sent us a receipt.
• Errors or Unusual Statuses: If a submission fails, or you see a green tick with any status other than ‘Fulfilled’, email support@clearbooks.co.uk so we can investigate with HMRC.

Received a Missing Update Letter from HMRC? 

If HMRC notifies you about missing updates but all required updates show as ‘Fulfilled’ when viewing your obligations, they are likely expecting submissions for additional income sources.

• Check Your HMRC Online Account: We strongly recommend logging into your HMRC online account to investigate. From there, you can view all registered income sources and check the status of your quarterly obligations for each one. You can also use the portal to close down income sources you no longer have (or that were created in error) and add any new income sources HMRC doesn't know about yet.
• Managing Multiple Income Sources in Clear Books: Remember that each income source requires a separate business account in Clear Books. For example, you will need one business profile for property income and a second one for self-employment income (ensure you select the appropriate plan when adding a new business).
• Still in Doubt?: If you are still unsure about what is required after checking your online account, we recommend contacting HMRC directly for clarification.