Most of the time FreeAgent’s year end works. You check the figures, press the button, and the accounts and corporation tax return go off. But FreeAgent only supports the parts of the return that a typical small trading company needs, and if your company has anything outside that, it either cannot file or should not be used to file.
That does not mean you have to leave FreeAgent. It means the year end needs doing another way.
Why FreeAgent cannot file some returns
FreeAgent builds your CT600 from the categories in your books. Anything that needs a part of the return it does not support has nowhere to go. FreeAgent publishes the cases in its help on corporation tax and its guide to preparing for filing, and says the list is not exhaustive. We have grouped them below.
Your company is the wrong size or type
- Not a micro-entity. FreeAgent only prepares micro-entity accounts. If your company meets two of turnover over £1 million, a balance sheet over £500,000 or more than 10 employees, it needs small company accounts instead, and FreeAgent will not stop you filing the wrong ones.
- Dormant companies. FreeAgent cannot file for a dormant company.
- The final period. The last period before a company stops trading cannot be filed through FreeAgent.
- Companies limited by guarantee are not supported for accounts or the CT600.
- Mismatched periods. If your corporation tax period does not line up with the accounting period at Companies House, for example after changing your year end, FreeAgent cannot file.
Income FreeAgent cannot handle
- Selling a business asset at a gain, such as a van, equipment or property, where there is a chargeable gain to report.
- Buying and selling investments, and any profit or loss on them.
- Dividends received from other companies or investment funds.
- Property rental income in the company.
These come up more than people expect. A company that has built up cash and started investing it, or bought a buy to let through the company, has usually moved outside what FreeAgent’s year end can do without anyone noticing.
Losses and reliefs
- R&D relief or the RDEC credit. FreeAgent does not support R&D claims on the CT600. Given how closely HMRC now checks them, this is not one to work around. Our guide to R&D tax credits for software companies covers the rules, including the claim notification deadline that catches first-time claimants.
- Carrying a trading loss back to an earlier year to get tax repaid.
- Old or large losses: trading losses from before 1 April 2017, or more than £5 million carried forward.
- Capital losses brought forward.
- Charitable donations. FreeAgent works out the tax correctly but cannot fill in the relevant box, so it says the return should not be filed through FreeAgent.
Director’s loans
Two situations here. FreeAgent cannot file the part of the return that reclaims S455 tax once a director’s loan has been repaid. And for loans made on or after 6 April 2026, where the S455 rate is 35.75 per cent, FreeAgent says the return cannot be filed through it before 6 April 2027, because HMRC’s system cannot accept the new rate until then.
Our guide to the director’s loan account in FreeAgent explains how FreeAgent works out the balance and what it leaves for you to fill in.
What to do instead
You do not have to move your books. The usual way this works:
- Keep using FreeAgent for the day to day: invoices, bank, expenses, VAT and payroll.
- Give your accountant access to your FreeAgent account. They work from the same figures you see.
- They prepare the year end accounts and the corporation tax return in their own filing software, including the parts FreeAgent cannot do, and file them for you.
- Any year end adjustments go back into FreeAgent, so next year starts from the right numbers.
The thing to avoid is filing what FreeAgent will let you file when part of your year is missing from it. An asset sale left out of the return, or micro accounts filed for a company that is not a micro, does not go away because the software accepted it.
The deadlines do not move
None of this changes when anything is due. For most private companies the accounts are due at Companies House nine months after the year end. The corporation tax return is due 12 months after the end of the accounting period, and the tax itself is due nine months and one day after it, which is earlier than the return.
If you find out late in the year that FreeAgent cannot file for you, that is the time to get help, not after the deadline. Late accounts start at £150 and reach £1,500 after six months.
FreeAgent cannot file it? We can, from your FreeAgent books
Keep FreeAgent for the day to day. We prepare and file the accounts and corporation tax return it cannot, including R&D claims, asset sales and property income. 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
FreeAgent fills in the CT600 from your books, and it only supports the parts of the return that a typical small trading company needs. If your company has R&D relief, a gain on an asset sale, investment or property income, losses carried back, or is dormant or ceasing to trade, the return needs parts FreeAgent does not support.
Yes. You can keep your bookkeeping, invoicing, VAT and payroll in FreeAgent. The year end accounts and corporation tax return are then prepared from your FreeAgent data and filed through other software.
No. FreeAgent only prepares micro-entity accounts under FRS 105. A company that is too large to be a micro-entity needs small company accounts prepared another way.
No. Accounts are due at Companies House nine months after your year end for most companies, the corporation tax return is due 12 months after the end of the accounting period, and the tax itself is due nine months and one day after it.