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How to file the Self Assessment tax return for limited company directors to HMRC from FreeAgent

This article explains how to file your completed Self Assessment tax return directly to HMRC through FreeAgent, if you're a limited company director.

To file your return, select 'Prepare to File Online' on any page of your Self Assessment return.


If your information is not complete, FreeAgent will warn you that you haven’t filled in all the required information.


Bear in mind that you must select 'No' for any sections of the tax return that you don't need to fill in.


Remember also that you can quickly navigate round the incomplete sections of the return using the menu on the right-hand side of the screen. You can tell which sections are incomplete by the orange exclamation mark icon.


Once your information is complete, we strongly advise doing a few last-minute checks:

1 Does FreeAgent support all the pages you need to fill in?

Check that you don't need to fill in a page that we don't currently support, such as:

2 Have you completed everything you need to?

Check that you’ve completed all the relevant pages, sections and boxes on your tax return. Remember, FreeAgent doesn’t know exactly which of these apply to you. You should also make sure that you’ve filed month 12 payroll and explained all your bank transactions for the tax year that you’re filing for.

3 Get your accountant to check it over

If you have an accountant who can access your account, get them to check over the self assessment return. They can even submit this on your behalf in FreeAgent.

Once you’ve double (and triple!) checked your return you can file with HMRC by selecting 'File online with HMRC'.


Enter your Government Gateway ID and password, then select 'Submit Self Assessment'.


And that's it! You've successfully filed your Self Assessment return to HMRC.

You'll see the status of the return marked as 'Pending' while FreeAgent sends and confirms the return with HMRC.


When this is complete the return status will be changed to 'Filed'.


When a Self Assessment return is filed directly to HMRC, or marked as filed (see below), the relevant tax basis period will be locked, restricting the changes that can made to transactions or items in that period. When you file your Self Assessment return directly with HMRC or mark it as filed in FreeAgent (see below), certain transactions relating to your tax return will be locked.

Printing your return

If you would like to print your Self Assessment tax return press ctrl + p (or cmd + p if you're using a mac). Depending on which browser you are using you may also have the option to create a PDF.

Marking the return as filed if you don't file through FreeAgent

If you don't wish to file your Self Assessment tax return through FreeAgent (for example if your accountant uses his/her own software to file the return), you can still mark it as filed in FreeAgent. Simply select 'Mark as Filed' on any of the tax return pages.


After you have filed

Problems with the return

If there is a problem with filing the return you will see a message on the main return page and the status will be marked as 'Rejected'.


There are a number of common reasons for returns failing to submit successfully, including:

  • a wrong Unique Tax Reference number
  • HMRC’s system is down
  • certain inaccuracies in the figures, such as putting tax taken off as an income figure without putting the income in itself - if HMRC returns any errors like these, FreeAgent will flag them to you.

Correcting mistakes on your return

If you’ve filed your Self Assessment return and then realise you’ve made a mistake, you will be able to unlock the return in FreeAgent so that you can change it. Remember that you must then file the amended return to HMRC.

To do this, select the 'Unlock Return' button on any of the tax return pages.


You can then make any necessary changes. Don’t forget to go through the filing process again once you have finished, so that HMRC has an accurate amended return for you. FreeAgent helps to remind you of this by showing the return as 'Unfiled' once again.


You can file your return up to a maximum of 9 times and all amended returns must be filed within 12 months of the original due date.

Correcting mistakes on returns marked as filed

Once a return has been marked as filed, if you discover a mistake you can still correct it. To do this, select the 'Mark as Unfiled' button on any of the tax return pages.


You can then make any necessary changes. Don’t forget to mark the return as filed again once you have finished. Make sure that the return in FreeAgent matches what was actually filed with HMRC.

Locking of data once your return is filed

Once you have filed your Self Assessment tax return with HMRC through FreeAgent, your dividends and journals to dividend accounts will be locked until the end of the tax year covered by your tax return. This means that you will be unable to create or amend any dividend payments and journals to dividend accounts that are dated before the end of the tax year.

If you use FreeAgent’s in-built payroll, your company’s payroll for that tax year will also be locked. FreeAgent locks these accounts because they should now be finalised and any changes to them would affect your tax return.

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