Stripe Reconciliations

If you receive automatic payouts from Stripe, DoubleAgent can reconcile them automatically for you in FreeAgent.

All you need do is connect your Stripe account(s) and DoubleAgent does the rest. All payments (and refunds) from your customers in Stripe will be explained in FreeAgent and all fees will be explained correctly too.

DoubleAgent can explain Stripe payouts in three different ways – just pick the one that suits you best:

  • with rolled-up sales transactions;
    • i.e. one explanation for all UK customers' charges in a payout, one for all EU customers', and one for everybody else's;
  • with one sales transaction per charge;
  • with one invoice per charge.

Please be aware that it's impossible to reconcile any payouts you create manually in Stripe, because Stripe itself doesn't know which charges and refunds were bundled into them.

What do we recommend?

If you need to keep track in FreeAgent of who paid you, use the invoices method.

Otherwise if you don't need to keep track of who's who, but you do need to see the individual charges in FreeAgent, use the sales-transaction-per-charge method.

Or, if you just need the overall amounts, use rolled-up sales transactions. (This is the simplest.)

How does it work?

Every time you receive a payout, DoubleAgent gets a breakdown from Stripe of everything making up that payout: customer payments, refunds, fees charged by Stripe, etc. DoubleAgent goes through the items as follows:

  • explaining with rolled-up sales transaction
    • DoubleAgent accumulates each charge in one of three buckets, depending on the customer's country – UK, EU, or everywhere else – and accumulates the fees.
    • After processing all the items in a payout, DoubleAgent creates one sales transaction for each bucket (with the correct VAT and EC status); one Stripe fee payment; and one Stripe application fee payment if needed.
  • explaining with one sales transaction per charge
    • After processing a charge, DoubleAgent create a sales transaction for it, a Stripe fee payment, and a Stripe application fee payment if needed.
  • explaining with one invoice per charge
    • After processing a charge, DoubleAgent finds the relevant contact in FreeAgent. If the contact doesn't yet exist, because it's a new customer, DoubleAgent creates it in FreeAgent using the information from Stripe. Once it has the FreeAgent contact, DoubleAgent looks for an invoice corresponding to the payment. If no such invoice exists, DoubleAgent creates it, again using the information from Stripe. Then DoubleAgent settles the invoice with funds from the payout. Finally DoubleAgent creates a Stripe fee payment, and a Stripe application fee payment if needed.

Before you start

First you have to tell FreeAgent not to guess explanations for your Stripe transactions. This leaves the transactions free to be explained by DoubleAgent.

If you have FreeAgent's Guess switched on for your bank account:

  • In FreeAgent go to your bank account's page, open the More dropdown (in the top-right corner), and click the Guess Rules link.
  • Go to the Excluded Terms tab.
  • Add the term Stripe to the list of excluded terms.

For more details see FreeAgent's How to manage Guess article, particularly the section How to exclude a transaction term.


DoubleAgent lists on the Logs page every change it makes to your FreeAgent account. All changes made when reconciling Stripe payouts – adding a contact, raising an invoice, explaining invoice receipts, explaining fees – refer to the Stripe payout reference. This makes it easy to see exactly what DoubleAgent is doing for you.

Undoing changes

Naturally you can undo any change DoubleAgent makes to your FreeAgent account. On your Stripe integration page, click the delete icon next to the explanation you want to undo.

More information