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

This article explains how to file your completed limited company director Self Assessment tax return directly to HMRC from within FreeAgent.

Preparing to file your Self Assessment tax return

First, navigate to the ‘Taxes’ tab at the top of the screen and select ‘Self Assessment’ from the drop-down menu.


Select the relevant user from the drop-down menu.


Select the relevant tax year from the list or from the ‘History’ drop-down menu.


To file your return, select 'Prepare to File Online' at the top of any page of your Self Assessment tax return.


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


Please note that you must select ‘No’ for any sections of the tax return that you don't need to fill in.


Use the ‘Your Tax Return’ menu on the right-hand side to navigate between the sections of your tax return. Incomplete sections are marked with an orange exclamation mark.


Once your information is complete, we strongly advise doing the following three 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 FreeAgent doesn’t currently support. These include:

If you need to complete any of these pages, you won't be able to use FreeAgent to submit your Self Assessment tax return.

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 which of these apply to you.

3. Ask your accountant to review your return

If you use FreeAgent with your accountant, ask them to check your Self Assessment tax return. They can even submit the return to HMRC on your behalf through FreeAgent.

Filing your Self Assessment tax return to HMRC

Once you’ve checked all of the information is completed and correct on your tax return, file it to HMRC by selecting 'File online with HMRC' in the top-right corner of your screen.


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


Once you’ve submitted your Self Assessment tax return, the status of the return is marked as 'Pending (locked)' while FreeAgent sends and confirms the return with HMRC.


Once this is complete and confirmed, the return status will be changed to 'Filed (locked)'.


When a Self Assessment tax return is filed directly with HMRC, or marked as filed, the relevant tax basis period will be locked, restricting the changes that can be made to transactions or items within that period.

Please note that it can take up to 72 hours for your tax return to be processed and updated on your HMRC account.

Why has my Self Assessment tax return failed to submit?

If there is a problem with filing the return, you will see an error message at the top of the ‘Main Return’ page and the status will be marked as 'Rejected'.


These are the most common reasons for returns failing to submit successfully:

  • a wrong Unique Tax Reference number
  • HMRC’s system is down
  • certain inaccuracies in the figures

Make the necessary correction(s) to your Self Assessment tax return. If there are inaccuracies in your figures, FreeAgent should flag these at the top of your return. Once you have made the necessary correction(s), select 'File Online with HMRC' again and follow the steps to file the return again with HMRC. The status of the return will be then marked as 'Pending (locked)' while FreeAgent sends and confirms the return with HMRC.

How do I correct mistakes on my tax return after it’s been filed to HMRC?

If you’ve filed your Self Assessment tax return but you need to make a correction, you will need to unlock the return in FreeAgent. To unlock your return, navigate to the relevant return and then select 'Unlock Return' in the top-right corner of any of the tax return pages.


Once the return is unlocked, you can make the necessary changes to any of the pages.

Once you have finished editing, you’ll need to complete the filing process again to submit your accurate amended return to HMRC. If you do not complete the filing process, the return will remain marked as ‘Unfiled’ in FreeAgent.


Please note that you can file your return up to a maximum of nine times and all amended returns must be filed within 12 months of the original due date.

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

If you don't file your Self Assessment tax return through FreeAgent - for example, if your accountant uses different software to file the return - you can still mark it as filed in FreeAgent by selecting 'Mark as Filed' on any of the tax return pages.


How do I correct mistakes on my tax return after it’s been marked as ‘Filed’?

If you discover a mistake on your Self Assessment tax return once it has been marked as ‘Filed’, you can still correct it. To do this, select the 'Mark as Unfiled' button in the top-right on any of the tax return pages.


Next, make any necessary changes and ensure that the return in FreeAgent matches what you filed with HMRC.

Once you have finished, select ‘Mark as Filed’ in the top-right corner.


Locking of data once your return is filed

As a limited company director, 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.

You will receive an error message if you try to create or amend any of the following items which are dated before the end of the basis period:

If you discover that you’ve made a mistake on your tax return, you will be able to file an amended return.

Opening balances in a locked period

If you create any new stock items or user mileage balances within a locked period, you will need to set an opening balance of zero, and you won't be able to change the opening balance of any existing bank accounts once your accounts are locked.

Opening balances that are created through the trial balance or by creating updated journal entries follow the same rules as any other journal entries, so you won't be able to enter any new opening balances or adjust your existing ones after your accounts are locked. New bank account opening balances are also locked.

Printing your Self Assessment tax return

You can print your completed Self Assessment tax return pages directly from your web browser by pressing either ‘ctrl + p’ if you’re using a PC or ‘cmd + p’ if you're using a Mac. Depending on your web browser, you may also be given the option to create a PDF.

You can also print a version of the SA302 form from the Self Assessment area of FreeAgent once you’ve completed and filed your tax return.

For information on how to explain a Self Assessment payment to HMRC, please see this article.

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