If you run a small limited company and keep your books in FreeAgent, you may have noticed that it offers to file your year end for you. It can. For a lot of one or two person companies it will produce the accounts, fill in most of the corporation tax return, and send both off at the click of a button.
What it will not do is tell you whether that is the right thing to file. That part is still on you.
The short answer
FreeAgent can file your company’s year end if your company is a micro-entity, is limited by shares, is trading, and none of the situations on its exclusions list apply. If all of that is true, many directors file their own year end in FreeAgent without an accountant.
If any of it is not true, FreeAgent either cannot file at all or should not be used to file, and you need the accounts and return prepared another way. The difficulty is that the software will not always stop you.
What FreeAgent can file for a limited company
According to FreeAgent’s own list of what it can file, a limited company can send:
- Final accounts to Companies House, prepared to FRS 105, the micro-entity standard.
- The corporation tax return (CT600) to HMRC, with the accounts and tax computations attached, including the CT600A supplementary page where a director’s loan was outstanding.
- VAT returns under Making Tax Digital.
- Payroll submissions, but only for a monthly payroll.
- Directors’ Self Assessment returns, for users with full access.
It cannot file the confirmation statement, which goes to Companies House separately, and it cannot file amended final accounts. It also does not handle P11D benefit returns or CIS returns as a contractor.
The software itself is £33 a month plus VAT for a limited company, or free for as long as you keep a NatWest, Royal Bank of Scotland or Ulster Bank business current account, or a Mettle account with at least one transaction a month. That is why so many directors have it without ever having chosen it.
The check FreeAgent does not do for you
FreeAgent only prepares micro-entity accounts. It does not check that your company is a micro-entity, and Companies House will not reject accounts filed on the wrong basis. So a company that has outgrown the micro limits can file micro accounts in FreeAgent and nothing will flag it.
For accounting periods beginning on or after 6 April 2025, a company is a micro-entity if it meets at least two of these size conditions:
| Condition | Micro-entity | Small company |
|---|---|---|
| Turnover | £1 million or less | £15 million or less |
| Balance sheet total | £500,000 or less | £7.5 million or less |
| Average employees | 10 or fewer | 50 or fewer |
The limits went up in April 2025. Before that the micro-entity turnover limit was £632,000, so a company that was too big last year may qualify now. Most owner managed companies sit comfortably inside these limits, but it is worth checking rather than assuming.
When FreeAgent cannot file
This is the part most directors never read. FreeAgent’s help on corporation tax lists situations where it cannot file the CT600, and it says the list is not exhaustive. The ones that come up most for small companies:
- R&D relief or the RDEC credit claimed on the return.
- Selling a business asset at a gain, or buying and selling investments.
- Dividends received from other companies or investment funds.
- Property rental income in the company.
- Carrying a trading loss back to an earlier year, or capital losses brought forward.
- Dormant companies, and the final period before a company stops trading.
- Companies limited by guarantee.
- Reclaiming S455 tax on a director’s loan that has been repaid.
- A corporation tax period that does not line up with the accounting period at Companies House.
We go through each of these, and what to do instead, in FreeAgent can’t file my accounts: what now?
There is one more that is new this year. S455 tax on an overdrawn director’s loan is 35.75 per cent for money drawn on or after 6 April 2026, but FreeAgent says HMRC’s systems cannot accept that rate until 6 April 2027, so a return that needs it cannot be filed through FreeAgent before then. The tax is still due on the normal date. If your loan account was overdrawn at your year end, read our guide to the director’s loan account in FreeAgent before you file.
What actually goes on the public record
When FreeAgent files your final accounts, it sends Companies House a shortened version, essentially the balance sheet, which is what currently goes on the public register for a micro-entity. Your profit and loss account is used for the tax return but is not published.
That is changing. From 1 April 2028, micro-entities and small companies will have to file a profit and loss account with Companies House, and accounts will only be accepted through software. What that means for FreeAgent users is in our guide to FreeAgent and the Companies House accounts changes.
So do you still need an accountant?
Honestly, not always. If your company is a straightforward micro-entity, your books in FreeAgent are genuinely up to date, and nothing on the list above applies, FreeAgent can do the filing.
Where an accountant earns their fee is everything around the filing:
- Checking the year end figures are right before they go anywhere. The accounts are only as good as the categorisation in FreeAgent, and a misfiled transaction becomes a wrong tax return.
- Picking up the cases above before you file, not after.
- Planning your salary and dividends before the year ends rather than recording them after. Our guide to salary and dividends in FreeAgent covers the numbers for 2026/27.
- Dealing with HMRC if a question comes back.
Keep FreeAgent. Have an accountant check it before it is filed
FreeAgent can press the button. We make sure what it sends is right, pick up the cases it cannot file, and plan your tax before the year closes. We work with limited companies only, inside your own FreeAgent account, so there is nothing to move. Fixed monthly fees from £145 + VAT, covering your year end accounts, corporation tax return and your own Self Assessment.
Book a Free ConsultationOr see our fixed-fee packages. We work with limited companies across Bedfordshire, Hertfordshire, Buckinghamshire and Northamptonshire, and remotely throughout the UK.
Frequently Asked Questions
Yes, if your company is an active company limited by shares that qualifies as a micro-entity, and none of the situations FreeAgent cannot handle apply. FreeAgent files micro-entity accounts to Companies House and the CT600 to HMRC from the data in your account.
No. FreeAgent prepares micro-entity accounts but does not check that your company qualifies, and Companies House will not reject accounts filed on the wrong basis. For accounting periods beginning on or after 6 April 2025, a micro-entity meets two of: turnover up to £1 million, balance sheet total up to £500,000, and 10 or fewer employees.
No. The confirmation statement is filed separately with Companies House. FreeAgent also cannot file amended final accounts.
No. FreeAgent does not support R&D relief or the RDEC credit on the CT600, so a company claiming R&D relief needs its return prepared and filed another way.
Yes. FreeAgent is free for as long as you keep a NatWest, Royal Bank of Scotland or Ulster Bank business current account, or a Mettle account with at least one transaction a month. Otherwise the limited company plan is £33 a month plus VAT.