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Switching From FreeAgent to CleanBooks AI

September 7, 2026 3 min read

Quick answer: You can switch from FreeAgent to CleanBooks AI at any point in the tax year. The main task is carrying your year-to-date income and expense totals across accurately so your next MTD quarterly update reflects the full picture, alongside reconnecting your bank feed in your new account.

Moving MTD software mid-year sounds more disruptive than it usually is, provided you’re careful about the handover of your figures. Here’s what actually matters when switching from FreeAgent.

Why people make this switch

The most common reason is wanting less manual categorisation. FreeAgent’s rule-based system requires you to review and code transactions yourself; CleanBooks AI’s Keeva assistant handles that automatically and improves as it learns your patterns. If you don’t bank with NatWest, RBS, Ulster Bank or Mettle (where FreeAgent is free), the price difference between the two also narrows or disappears, which removes what’s often FreeAgent’s biggest advantage.

Before you switch

  • Export your year-to-date income and expense figures from FreeAgent so you have a clean record of everything reported in your MTD quarterly updates so far this tax year.
  • Check which quarterly updates you’ve already submitted to HMRC; these don’t need to be resubmitted, only your next update needs to carry the correct cumulative figures forward.
  • Note any outstanding invoices or unreconciled transactions in FreeAgent so nothing gets lost in the move.

Setting up CleanBooks AI

Connect your bank account via open banking, and let Keeva begin categorising your transaction history. For the period already reported through FreeAgent, you’ll typically enter the confirmed year-to-date totals directly rather than re-processing every historical transaction, since HMRC already has those figures from your earlier submissions. See how AI bookkeeping works for how Keeva handles ongoing categorisation from this point.

Timing the switch

The cleanest time to switch is right after submitting a quarterly update, so you’re starting the new quarter with a clear cut-off point. Switching mid-quarter is possible but means more careful reconciliation to make sure nothing from that partial quarter is double-counted or missed.

Ready to stop juggling spreadsheets? Start your free trial of CleanBooks AI today.

Frequently asked questions

Will HMRC be notified automatically when I switch software?
No, there’s no need to notify HMRC separately; you simply submit your next quarterly update through your new software once it’s set up.
Can I keep using FreeAgent for anything after I switch?
Once you’ve exported what you need and confirmed your figures have carried across, most people cancel their FreeAgent subscription, though it’s worth keeping historical exports for your own records.
Is there a free trial to test CleanBooks AI before fully switching?
Yes, see our free trial page for current details, so you can see how the categorisation works with your own transactions before committing.
What if I have invoices still outstanding in FreeAgent?
Settle or record these before switching where possible, or make sure they’re accounted for manually in your new software so income isn’t missed from your records.

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