FreeAgent has a built-in Stripe integration. If you're considering using it, or you're already using it and wondering if it's enough, here's an honest breakdown of what it does, what it doesn't do, and when you might need something more.
What it does
FreeAgent's native Stripe integration creates a Stripe bank account in your Banking area and imports balance transactions automatically. Here's what that gives you:
Automatic transaction import. Once connected, FreeAgent pulls in your Stripe balance transactions each morning. Charges, fees, and refunds appear as unexplained transactions, just like a normal bank feed.
Invoice matching. If you've created an invoice in FreeAgent and a customer pays it via Stripe, FreeAgent can match the payment to the invoice. The invoice is marked as paid and the transaction is explained.
Fee tracking. Stripe fees appear as separate transactions. You can explain them as expenses under "Bank & Finance Charges" (or whatever category you prefer).
Payout reconciliation. When Stripe sends a payout to your bank account, the Stripe bank account shows a corresponding outgoing transfer. You can match this against the deposit in your real bank account.
For a business that invoices through FreeAgent and uses Stripe payment links to collect payment, this workflow is straightforward. Create invoice, send payment link, payment arrives, invoice is marked paid.
What it doesn't do
The native integration has some significant limitations. If any of these matter to you, you'll need a different approach.
No multi-currency support. The Stripe bank account only imports transactions in your FreeAgent base currency (usually GBP). If you hold EUR, USD, or other currency balances in Stripe, those transactions are ignored entirely. You'll see the payout when it hits your bank, but not the underlying charges and fees.
No invoice mirroring. If your invoices are created in Stripe (subscriptions, Checkout sessions, or Stripe-generated invoices), FreeAgent doesn't see them. You only see the payment. The line items, product details, and customer information from the Stripe invoice aren't imported.
No per-product categorisation. All Stripe income lands in whatever category you assign when explaining the transaction. There's no way to automatically categorise revenue by Stripe product. If you sell multiple products, your P&L shows a single line for all Stripe income.
One Stripe account only. You can't connect multiple Stripe accounts to a single FreeAgent account. If you run separate Stripe accounts for different businesses or brands, you can only integrate one.
Manual refund handling. Refunds appear as transactions, but they're not automatically linked to the original charge or invoice. You'll need to explain each refund manually.
No credit note support. When Stripe issues a credit note (for a partial refund or billing adjustment), FreeAgent doesn't create a matching credit note. You'll need to handle this manually.
When the native integration is enough
The native integration works well if:
- You create invoices in FreeAgent and use Stripe payment links to collect payment
- All your Stripe transactions are in GBP
- You don't need revenue broken down by product
- You have one Stripe account
- Transaction volume is low enough that manual explanation is manageable
This describes a lot of small businesses. If it describes you, the native integration is free and does the job.
When you need something more
The native integration falls short if:
- You run subscriptions through Stripe Billing and want invoices in FreeAgent
- You use Stripe Checkout and need line item detail in your accounts
- You accept payments in multiple currencies
- You want your P&L to break down revenue by product
- You have multiple Stripe accounts to connect
- You want refunds and credit notes handled automatically
If any of these apply, ClearingHouse fills the gaps. It syncs Stripe invoices into FreeAgent with full line item detail, supports multiple currencies with per-currency clearing accounts, lets you map products to accounting categories, and handles refunds and credit notes automatically.
Switching from the native integration
If you're currently using FreeAgent's native Stripe feed and want to switch to ClearingHouse, you'll need to disconnect the native integration first to avoid duplicate transactions.
ClearingHouse lets you choose a sync start date, so you can pick up where the native integration left off without re-importing transactions that are already in FreeAgent.
Setting up ClearingHouse takes a few minutes. Connect your Stripe and FreeAgent accounts, configure your settings, and your data will start syncing automatically.
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