What can you file using FreeAgent?

This article provides a summary of the tax and other forms that can be filed to Companies House or HMRC using FreeAgent.

The following tax and other official forms can be filed using FreeAgent:

End of Year accounts

FreeAgent’s End of Year functionality for limited company account types has two components: the Final Accounts report and the Corporation Tax return.

Final Accounts report

The Final Accounts (FRS 105 micro-entity accounts) report in FreeAgent is prepared according to the financial reporting standard for companies that meet the official definition of a ‘micro-entity’.

The report will display the company’s Income Statement and Balance Sheet figures and will be initially marked as ‘Draft’ until you've added the necessary notes to the accounts to finalise the report.

If your business meets the official definition of a micro-entity, you can use this report to submit your annual accounts to Companies House and HMRC. Please note that FreeAgent won’t indicate whether your company qualifies to prepare accounts under FRS 105 or not.

FreeAgent will file a shortened version of your accounts to Companies House. The term ‘Abbreviated’ in FreeAgent refers to ‘shortened accounts’ and is not included in the title of the accounts that are filed with Companies House.

If FRS 105 micro-entity accounts are filed through FreeAgent by mistake when your company does not qualify to use FRS 105, these will not be automatically rejected by Companies House. Companies House will check some of the data on the accounts, such as the name, signature and reporting period, but it won’t check if the right accounting standards have been applied when preparing the accounts. It is the responsibility of the company directors to make sure that the accounts have been prepared correctly.

If you’ve already filed your original end of year accounts, and need to submit amended accounts to include any changes, please note that it’s not currently possible to file amended Final Accounts through FreeAgent. You’ll need to file your amended accounts with Companies House directly if you make any changes to your Final Accounts. Please see this official guidance for more information.

Corporation Tax return

FreeAgent uses the financial data entered throughout the year to populate most of your company’s Corporation Tax return (CT600). If you need to, you can adjust the Corporation Tax liability figures.

If you need to report a year-end debit balance on your director’s loan account to HMRC - in other words, money that you owe to the company - you can enable the CT600A supplementary pages.

Please note that at the moment, there are certain Corporation Tax scenarios which are unsupported in FreeAgent.

You might find the following articles from our Knowledge Base useful for dealing with Corporation Tax in FreeAgent:

Filing your End of Year accounts through FreeAgent

Before you file your Final Accounts and Corporation Tax (CT600) return for the first time through FreeAgent, make sure that you’ve completed these steps.

We strongly recommend asking an accountant to review your accounts and tax returns before submitting them to HMRC.

You might find the following articles from our Knowledge Base useful if you receive an error message when filing your End of Year accounts:

If you have filed your End of Year accounts outside of FreeAgent, you can manually mark your Final Accounts report and Corporation Tax (CT600) return as filed.

Making corrections to your End of Year accounts

If you find that there are errors within your accounts after you’ve filed or marked as filed your Final Accounts and/or Corporation Tax return, you can either unlock your End of Year report to make the corrections this year or make the corrections next year.

Find out how to make corrections after filing End of Year reports.


If your business has employees, or you’re paid a salary as a limited company director, you must register as an employer with HMRC and work out your salaries, then tell HMRC how much you’ve paid and to whom using RTI (Real Time Information) submissions.

FreeAgent supports monthly payroll RTI submissions and does not currently support weekly or annual payroll filing.

Please note that FreeAgent's payroll functionality won't be available if you're preparing your accounts using cash basis accounting, or if you have an unincorporated landlord or non-UK account type.

If you or your accountant file payroll outside of FreeAgent, you can prepare your payroll and then mark it as filed instead of filing it to HMRC through FreeAgent.

If you’re currently filing payroll outside of FreeAgent and moving your payroll to FreeAgent during the tax year, find out how to move your payroll to FreeAgent from another software provider.

Setting up payroll

To set up payroll in FreeAgent, you’ll need to have full (level 8) access to your FreeAgent account. Each employee that will be included on your payroll will need to be added as a user in FreeAgent.

Please note that if you have a sole trader account and you're the only user on the account, you won't have access to payroll until you've added users with the role of ‘Employee’. This is because, as a sole trader, you will take drawings from the business, not a salary.

You might find the following other articles from our Knowledge Base useful for setting up payroll in your account:

Running payroll

You might find the following articles from our Knowledge Base useful for running payroll in your FreeAgent account:

Making payroll corrections

Once you’ve filed payroll to HMRC using FreeAgent, it’s not possible to delete or undo the payroll submission. However, if you need to make any corrections to an employee’s pay or deductions in the current tax year after filing the payroll, you can edit the relevant payslip, which will submit the correct year-to-date figures to HMRC in your next submission.

If you need to make corrections in a previous tax year or to a month 12 payslip, find out how to make a payroll correction for a previous tax year.

Statutory pay

FreeAgent supports the reclaiming of statutory maternity pay, statutory paternity pay, statutory adoption pay, statutory parental bereavement pay and shared parental pay.

Statutory sick pay can be entered into a payroll profile and onto a payslip in FreeAgent but will not be reclaimed, since HMRC no longer permits this. Please note that you’ll need full (level 8) access to FreeAgent to add statutory pay to a payroll profile or payslip.

FreeAgent also supports the full 103% reclaim of statutory parental pay for small employers.

Please note that if your business does not qualify as a small employer and can only reclaim 92% of statutory parental pay, you will not be able to use FreeAgent’s payroll. Instead, you’ll need to file your payroll outside of FreeAgent and create journal entries to record the payroll in your FreeAgent account.

Find out more about how FreeAgent handles statutory pay.

HMRC form P11D

You can't prepare forms P11D or P11D(b) in FreeAgent.

Find out how to record the liability in your FreeAgent account, and how to explain the NI payment to HMRC.

Construction Industry Scheme (CIS)

The Construction Industry Scheme requires contractors to deduct income tax when they settle invoices presented by their subcontractors. FreeAgent supports CIS for subcontractors who are sole traders or operating through limited companies. You can also record the CIS transactions if you are a contractor, but FreeAgent doesn’t support CIS payroll filing for contractors.

If you are both a contractor and a subcontractor, find out more about how to record CIS transactions in FreeAgent.

Please also note that FreeAgent does not fully support CIS for partnerships or unincorporated landlords. Find out more on how to record CIS transactions in your partnership accounts.

Self Assessment

Self Assessment is the area of FreeAgent where income tax and National Insurance are worked out for a personal Self Assessment tax return. This will be based on your business's accounts if you're a sole trader, your salary and dividends if you're a director of a limited company or your property income and costs if you’re an unincorporated landlord.

You might find the following articles from our Knowledge Base useful for dealing with Self Assessment in FreeAgent:

Filing Self Assessment using FreeAgent

FreeAgent supports the filing of Self Assessment tax returns for sole traders, limited company directors and unincorporated landlords with full (level 8) access.

Please note that if you're a partner (with either a Partnership or Limited Liability Partnership account type), secretary, shareholder or employee, you won't be able to use FreeAgent to file Self Assessment to HMRC. However, you may be able to refer to the information that FreeAgent generates in your FreeAgent account when you come to complete your tax return.

Before you can file your Self Assessment tax return, you’ll need to make sure that all of your bank transactions have been explained for the tax year that you’re filing for. If you’ve been running payroll, you’ll also need to have filed or marked as filed month 12 payroll for the tax year in question.

You might find the following Knowledge Base articles useful for filing Self Assessment in FreeAgent:

If you find that there are errors on a Self Assessment return after you’ve filed it to HMRC through FreeAgent, you can unlock the return to make the corrections and submit an amended return if it’s within HMRC’s deadline for making corrections. Find out how to correct a locked Self Assessment tax return in FreeAgent.

Once you've filed your Self Assessment tax return and paid your tax bill to HMRC, find out how to explain a Self Assessment payment to HMRC.

Partnership tax returns

Each partner in a partnership must fill in the Partnership (SA104) section of their Self Assessment tax return. In addition, one partner will have to complete a separate Partnership Tax Return (SA800) for the partnership.

HMRC provides notes about the SA104 that may help you determine if you have to complete this section.

Please note that at the moment, FreeAgent does not support the filing of partnership tax returns.

HMRC itself does not support the filing of partnership tax returns directly through its portal, but it does provide a list of third party software providers that may be of help. You’ll need to find software that says it supports an ‘SA800’, which is the partnership tax return. Alternatively, your accountant may have third-party software which they can use to submit your return to HMRC.

FreeAgent does use the information in your FreeAgent account to produce estimated figures for the individual partners and you may be able to use these figures to help you file the tax return outside of FreeAgent. You can edit the partnership profit share if you need to.

If your partnership accounting year ends on 5th April, the Self Assessment section should give you all of the information you need. However, you would also need to check the capital allowances as this is only a ballpark calculation in FreeAgent.

On the other hand, if your partnership accounting year ends on a date other than 5th April, you would need to review the Profit and Loss (P&L) report. This is because the Self Assessment pages for a partnership in FreeAgent always prepare the accounts to 5th April, even if the partnership has a different year end. Therefore, you’d need to start by using the P&L figures to help you complete your tax return. You could also use the Capital Assets report to identify any assets on which you could claim capital allowances.

Please bear in mind that the P&L report contains the figures for the entire partnership, so if you’re completing your own partner tax return, you should be careful to only include your share of the partnership’s income and profit.


You can file VAT returns to HMRC using FreeAgent’s Making Tax Digital (MTD) for VAT connection.

You’ll need to have full (level 8) access to your FreeAgent account and set up the MTD for VAT connection with HMRC. To create your VAT returns, FreeAgent needs to have the details of all of your bank transactions, invoices, bills and out-of-pocket expenses, entered and explained correctly. Find out more about how to prepare for Making Tax Digital (MTD) for VAT in FreeAgent.

Please note that you'll only be able to file a VAT return to HMRC once the VAT period has ended. For example, if the VAT period ends on 31st August, you'll be able to file the return from 1st September onwards.

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