You’ve missed the MTD deadline… now what?

With all the new information you’re taking in about Making Tax Digital (MTD) for Income Tax, getting a little scrambled about the different dates and deadlines is understandable! Don’t panic, now you’ve realised you’ve missed a deadline, you can take the right steps to fix the mistake.  

We’ve looked into the consequences of missing each deadline in the first year of MTD for Income Tax. So, without further ado, which deadline have you missed? 

You’ve missed the sign-up deadline

If you’re a sole trader or landlord with a turnover of more than £50k, you should have signed up for MTD for Income Tax by 6th April 2026. If you haven’t done so yet, you are late. 

Don’t worry, however, you still have time to get on top of MTD for Income Tax. HMRC has confirmed they won’t issue penalty points or fines for missing this deadline. 

That doesn’t mean you can ignore MTD, though. The sooner you sign up, the easier it will be to make sure your records are MTD-compliant and to avoid any future fines. Follow our step-by-step sign-up guide to get registered and link your accounting software to HMRC. 

You’ve missed the first quarterly update deadline

The first quarterly update deadline for those who signed up to MTD in April 2026 is 7th August 2026. If you miss that milestone, that’s okay, there’s still time. As it is your first year of MTD for Income Tax, HMRC won’t issue a penalty point.

As soon as you can, make sure you’ve entered all your income and costs for the first quarterly update period (usually 6th April - 5th July). The easiest way to do this is by connecting your business bank account to FreeAgent to automatically pull through your transactions. Once that’s done, check they’re accurate and assigned to the correct categories. Then just double-check the numbers look correct in your quarterly update, and submit it late to HMRC.  

You’ve missed multiple quarterly update deadlines

You’re a bit late to the party - and you are going to have some catching up to do - but you’re in luck! HMRC won’t issue any penalty points for quarterly updates in your first year, so you have time to catch up before they start introducing fines. 

If you’ve missed several quarterly updates, you’ll have to submit each one in order, starting with the first quarter (6th April - 5th July). Make sure you add all your income and costs to your accounting software before you submit these. Then you’ll be able to check the numbers and submit them to HMRC. 

You’ve missed your final Self Assessment deadline

During your first year of MTD, the new system will overlap with Self Assessment - the old way you’ve been used to filing your taxes annually. 

You still have to submit your final Self Assessment tax return by 31st January 2027 - and if you miss the deadline, late filing penalties will apply. That means if you file your Self Assessment for the 2025/26 tax year late, you’ll immediately face a £100 penalty. 

If your Self Assessment return is more than three months late (i.e. you file after 30th April 2027), you’ll get additional daily penalties of £10 per day, up to £900. If you file more than six months late (i.e. after 31st July 2027), you’ll get an additional penalty of 5% of the tax due or £300 (whichever is the higher amount). And after 12 months, there’s another penalty! 

Your deadline for paying your tax owed for 2025/26 is also 31st January 2027 - and there are additional fines for paying late.

So it’s really important that you submit your Self Assessment return as soon as possible, and pay your tax bill, so you don’t end up with a huge fine.

You’ve missed the MTD tax return deadline

The deadline for the first MTD tax return (sometimes also referred to as a ‘final declaration’) is 31st January 2028. If you miss it, HMRC will issue you a penalty point. You won’t receive any fines until you reach four points, so you have time to get on top of your tax deadlines and avoid racking up more points.

You won’t be able to submit your tax return until all your quarterly updates are submitted, so make sure they’re complete. (If you’ve also missed your quarterly update deadlines, go back and follow the steps for missed quarterly updates first.) 

In FreeAgent, you’ll need to submit two parts - an end-of-year update and a final declaration. To submit these, you’ll need details of your total income for the year - not just your MTD-qualifying income. This is also the point you can add details of any reliefs you’re eligible for. 

If you’ve missed the MTD tax return deadline, you’ve also missed the payment deadline

As with the old system of Self Assessment, your payment deadline under MTD is the same date as your tax return deadline - 31st January. If you’ve missed the payment deadline and it’s your first year of MTD for Income Tax, then you’ll have 30 days from the payment due date (31st January 2028) to make the payment. 

If your payment is more than 30 days late, you’ll be hit with the new late payment penalties. These are calculated as a proportion of the amount of tax you owe - 3% of your 2026/27 tax bill. There’s also an annual rate of 10% per year on the outstanding amount, which will be charged to you daily from day 31 until the tax is paid. So best to settle up with HMRC as soon as you realise your payment is late!

You can find out more information about late payment penalties under MTD for Income Tax on HMRC’s website.

No more missed deadlines with FreeAgent

We’re here to make MTD for Income Tax as simple as possible - and that means reminding you when a deadline is coming. Your personal FreeAgent Tax Timeline shows when your next submissions are, so you never miss another deadline.

And you can check all your important MTD dates in our blog, and add them to your own calendar with one handy download link.