FreeAgent common mistakes and how to fix them
The eight bookkeeping mistakes we see most often in FreeAgent, why they matter, and the safe way to put each one right.
By In Front Accounting, ACCA-qualified accountants · Published 21 October 2026
The short answer
- Most FreeAgent problems come down to two things: recording the same money twice, or explaining it the wrong way.
- Fix the underlying record (the explanation, expense or invoice) rather than adding a correcting entry on top.
- Be cautious with deleting: removed explanations and deleted bank transactions can't be recovered.
- Fix VAT errors before you file. Once a return is filed, ask your accountant how to correct it.
The mistakes, and the safe fix for each
1. 'Marked as sent' but the customer never got the invoice
What goes wrong: Mark as Sent only changes the status in FreeAgent. It doesn't email anything.
How to fix it: Open the invoice and use Actions > Send by email, choose the recipient, check the email and send. See our invoice guide.
2. The same payment recorded twice
What goes wrong: A manual bank entry was added, then the bank feed imported the same transaction.
How to fix it: Check the Manually Added tab. FreeAgent's Guess merges a manual entry with an imported one of the same amount, in the same account, dated within a day. A duplicate that can't be matched may need deleting, but FreeAgent recommends deleting only in limited cases and it can't be undone, so check first.
3. A receipt entered twice
What goes wrong: The cost was added as an out-of-pocket expense and the business bank payment was also explained as a cost. Or the same receipt was captured twice.
How to fix it: Keep one record. If the business bank paid, keep the bank explanation and remove the extra expense. See our expenses guide.
4. A bank transaction explained wrongly
What goes wrong: For example, a customer payment allocated to the wrong invoice, or a cost in the wrong category.
How to fix it: Find the bank transaction and remove the explanation (FreeAgent calls it Remove this Explanation), then explain it again correctly. You need level 6 access, and a removed explanation can't be recovered.
5. Approving Guess suggestions without looking
What goes wrong: Transactions in the For Approval tab already have a suggested explanation, which may be wrong.
How to fix it: Open each one in the For Approval tab, correct the Type or Category if needed, then approve it. Correct approvals also improve future guesses.
6. Bank feed gaps or delays
What goes wrong: A feed disconnected, or a transaction hasn't appeared yet, so someone adds it by hand.
How to fix it: Reconnect the feed, or upload a statement to fill the gap, rather than typing transactions in. Then compare FreeAgent's balance with your statement. See our bank reconciliation guide.
7. Wrong VAT treatment
What goes wrong: A zero-rated, exempt or non-VAT item recorded at 20%, or VAT reclaimed without a valid VAT receipt.
How to fix it: Correct the explanation, expense or bill before the VAT return is filed. If the return is already filed, speak to your accountant first; corrections follow HMRC's rules. See our VAT return guide.
8. Personal spending treated as a business cost
What goes wrong: Personal shopping paid from the business account and put in a cost category.
How to fix it: Re-explain it using an option such as Money Paid to User rather than a cost category. If you're unsure which option is right, ask your accountant.
Before you fix anything
- Note down what you're changing and why, in case you need to retrace it.
- If the transaction falls in a period whose VAT return is filed, or whose accounts are finished, check with your accountant first.
- For a big tidy-up, consider exporting a copy of your data first (Settings > Export All Data, which needs full access).
Want a qualified accountant to put your FreeAgent right?
We can review your account, fix errors and agree a fixed fee for ongoing checks. See our FreeAgent accountant service or send us a message.
Related Articles
Common Questions
Does 'Mark as Sent' email the invoice in FreeAgent?
No. It only changes the invoice status. To email it, use Send by email from the invoice.
How do I fix a payment matched to the wrong invoice?
Find the bank transaction, remove its explanation, then explain it again as an Invoice Receipt against the correct invoice.
Should I delete duplicate bank transactions?
Only in limited cases, such as a manually added duplicate that can't be matched to an imported transaction. Deletion can't be undone, so check first.
Can I correct a VAT mistake myself?
Before filing, correct the underlying record and the return updates. After filing, speak to your accountant, because corrections depend on HMRC's rules.
Last reviewed 21 October 2026. Steps follow FreeAgent's own help articles at the time of writing; menu names and access levels can change. Sources: FreeAgent: remove a bank transaction explanation, delete bank transactions, how Guess explains transactions, send an invoice to a contact. General guidance, not advice on your specific circumstances.