If you use Stripe for payments and FreeAgent for accounting, you've probably wondered how to connect them. There are three main options: FreeAgent's built-in Stripe integration, DoubleAgent, and ClearingHouse.
Each takes a different approach and suits different workflows. Here's an honest comparison.
FreeAgent's native Stripe integration
FreeAgent has a built-in Stripe bank feed that creates a Stripe account in your Banking area and imports transactions automatically.
How it works:
When you connect Stripe to FreeAgent, it creates a Stripe clearing account and imports balance transactions each morning. If a transaction matches an open FreeAgent invoice, FreeAgent can link them. Otherwise, you'll need to explain each transaction manually, just like a normal bank feed.
Best for:
- Businesses that invoice through FreeAgent and use Stripe payment links to collect payment
- Simple setups with one Stripe account and GBP-only transactions
- Low transaction volumes where manual review is manageable
Limitations:
- Single currency only. The Stripe clearing account only imports transactions in your FreeAgent base currency. Non-GBP balance transactions are ignored. Payouts to your real bank accounts still appear in those accounts, but without the underlying transaction breakdown.
- One Stripe account. You can't connect multiple Stripe accounts to one FreeAgent account.
- No invoice mirroring. If your invoices are created in Stripe (subscriptions, Checkout, etc.), FreeAgent doesn't see them. You only see the payment, not what it was for.
- Limited refund handling. Refunds aren't automatically explained. You'll need to categorise them manually.
- No per-product categorisation. All revenue lands in a single category. You can't break down sales by product.
Cost: Free (included with FreeAgent)
DoubleAgent
DoubleAgent is a third-party integration that reconciles Stripe (and GoCardless) payouts in FreeAgent using a rule-based system.
How it works:
DoubleAgent processes each payout by breaking it down into its component transactions: charges, fees, and refunds. It creates invoices or sales transactions in FreeAgent for each charge, records fees as expenses, and explains the payout.
You can choose between three reconciliation methods:
- One invoice per charge
- One sales transaction per charge
- Rolled-up aggregated transactions (all charges combined into summary records)
Best for:
- Businesses that want some automation but prefer aggregated sales records over individual invoices
- Workflows that need GoCardless reconciliation alongside Stripe
- Users who want receipt/invoice attachment features
Limitations:
- No per-product categorisation. Revenue isn't broken down by Stripe product. All sales use the same category.
- 30-minute sync delay. DoubleAgent syncs with FreeAgent every 30 minutes, not in real-time.
- Rolled-up transactions lose detail. If you use aggregated mode, you lose visibility into individual customer transactions.
- No Stripe invoice line items. When creating FreeAgent invoices, product and price details from Stripe aren't carried over.
- Manual setup for multi-currency. Multi-currency is supported, but transactions are bucketed into "UK or everywhere else" rather than tracked per currency.
Cost: £7-9/month depending on business type, or £10 + £9/client for accountancy practices
ClearingHouse
ClearingHouse syncs Stripe data into FreeAgent with full invoice mirroring, per-product categorisation, and multi-currency support.
How it works:
ClearingHouse uses Stripe webhooks to sync transactions as they happen. Every Stripe invoice creates a matching FreeAgent invoice with the same line items. Payments are recorded against those invoices. Fees are tracked separately. Payouts reconcile automatically.
For each currency in your Stripe balance, ClearingHouse creates a dedicated clearing account in FreeAgent. This means GBP, EUR, and USD transactions are tracked independently with proper currency handling.
Best for:
- SaaS businesses running subscriptions through Stripe Billing
- Anyone using Stripe Checkout or Stripe-generated invoices
- Businesses accepting payments in multiple currencies
- Users who want their P&L to break down revenue by product
Limitations:
- FreeAgent only. No support for Xero, QuickBooks, or other accounting software (yet).
- Stripe only. No GoCardless or other payment processor support.
Cost: £10/month, or £15 + £10/client for accountancy practices
Feature comparison
| Feature | FreeAgent Native | DoubleAgent | ClearingHouse |
|---|---|---|---|
| Sync method | Daily import | 30-min polling | Real-time webhooks |
| Invoice mirroring | No | Basic | Full (with line items) |
| Per-product categories | No | No | Yes |
| Multi-currency | No (base currency only) | Partial | Yes (per-currency clearing accounts) |
| Stripe fee tracking | Yes | Yes | Yes |
| Refund handling | Manual | Automatic | Automatic |
| Payout reconciliation | Automatic | Automatic | Automatic |
| GoCardless support | No | Yes | No |
| Receipt attachments | No | Yes | No |
| Price | Free | £7-9/month | £10/month |
Which should you choose?
Use FreeAgent's native integration if:
- You invoice through FreeAgent and customers pay via Stripe payment links
- All your transactions are in GBP
- You have low volumes and don't mind some manual categorisation
Use DoubleAgent if:
- You need GoCardless reconciliation alongside Stripe
- You prefer aggregated sales records over individual invoices
- Receipt attachment is important to your workflow
Use ClearingHouse if:
- You run subscriptions or use Stripe Checkout
- You want your P&L to break down revenue by product
- You accept payments in multiple currencies
- You want Stripe invoices properly mirrored in FreeAgent
If this sounds like you, try ClearingHouse free for 14 days.
Switching between options
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. ClearingHouse creates its own clearing accounts for each currency, so you don't want duplicate transaction imports.
ClearingHouse lets you choose a sync start date, so you can avoid duplicating transactions that are already in FreeAgent.
Getting started with ClearingHouse
If ClearingHouse sounds like the right fit, it takes a few minutes to set up. Connect your Stripe and FreeAgent accounts, map your products to accounting categories, and your data will start syncing immediately.
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