Stripe subscriptions generate a steady stream of invoices and charges. Reconciling them in FreeAgent means making sure each payment is properly recorded, fees are tracked, and your P&L reflects what you actually earned.
Here's how the native FreeAgent integration handles subscriptions, where it falls short, and how ClearingHouse fills the gaps.
What Stripe creates for each subscription charge
Every billing cycle, Stripe Billing:
- Creates and finalises an invoice with line items for the subscription
- Charges the customer's payment method
- Deducts its processing fee
- Adds the net amount to your Stripe balance
If a customer changes plan mid-cycle, the next invoice includes prorated line items. If they cancel and you issue a refund, Stripe creates a credit note. These are all just variations on the same pattern: Stripe creates invoices and charges, and your accounting needs to reflect them.
How FreeAgent's native Stripe integration works
FreeAgent has a built-in Stripe feed that imports balance transactions into a Stripe bank account. For subscriptions, this means:
- Each successful charge appears as a transaction
- Stripe fees appear as separate transactions
- You can explain each transaction by matching it to a FreeAgent invoice or categorising it directly
The limitation is that FreeAgent doesn't see the Stripe invoice. It only sees the payment. If you want proper invoices in FreeAgent (for accounts receivable, for your records, or because your accountant expects them), you need to create them yourself.
For each subscription charge, you'd need to:
- Look up the Stripe invoice to see what was charged
- Create a matching invoice in FreeAgent with the same line items
- Mark it as paid when the payment appears in your Stripe feed
At low volumes this is manageable. At 50+ subscribers on monthly billing, it's a significant time sink.
What you lose without invoice mirroring
If you skip creating invoices and just categorise each payment directly, you lose:
- Line item detail. A payment for "£49" doesn't tell you if that's one product or three. Prorated charges are just numbers without context.
- Per-product revenue. If subscriptions include multiple products, you can't break down revenue by product on your P&L.
- Accounts receivable. Without invoices, you have no record of unpaid subscriptions. Failed payments are invisible until you check Stripe.
For some businesses this is fine. For others, it's a gap that matters.
How ClearingHouse handles subscriptions
ClearingHouse syncs Stripe invoices into FreeAgent automatically. When Stripe finalises a subscription invoice, ClearingHouse creates a matching invoice in FreeAgent with the same line items, amounts, and customer details.
When the charge succeeds, the payment is recorded against the invoice. The Stripe fee is recorded as an expense. If Stripe issues a credit note, ClearingHouse creates a matching credit note in FreeAgent.
You can map each Stripe product to a FreeAgent accounting category, so subscriptions with multiple products have their revenue broken down correctly on your P&L.
The result is that your FreeAgent data matches your Stripe data. Invoices exist for every subscription charge. Payments are tracked against those invoices. Fees are recorded. You don't need to cross-reference Stripe to understand what a payment was for.
Which approach is right for you
Use the native integration if:
- You're comfortable categorising payments without underlying invoices
- You don't need per-product revenue breakdown
- You have low enough volume that manual invoice creation is feasible
Use ClearingHouse if:
- You want Stripe invoices mirrored in FreeAgent automatically
- You need your P&L to break down subscription revenue by product
- You'd rather not spend time on manual data entry every month
If that sounds like you, ClearingHouse takes a few minutes to set up. Connect your Stripe and FreeAgent accounts, map your products to categories, and your subscription invoices will start syncing automatically.
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