FreeAgent Shopify integration discontinued: what to do now

FreeAgent switched off its Shopify integration on 30 April 2025. Its own help article, Managing Shopify transactions in FreeAgent, says that for Shopify transactions from 1 May 2025 you need to record them yourself. The FreeAgent app is no longer available on the Shopify App Store.

If your Shopify sales stopped appearing in FreeAgent, nothing is broken on your side. Here are the options that exist today, cheapest first.

Option 1: explain each payout by hand (free, what FreeAgent recommends)

FreeAgent's article says that because Shopify already handles the invoicing, you usually do not need sales invoices in FreeAgent. Instead, when a Shopify payout lands in your bank feed, you explain it as Sales with the right VAT rate. If fees were taken, you split the transaction and explain the fee to Bank / Finance Charges. Refunds are split out and explained as Money out > Sales Refund.

Cost: free.
Good for: a few payouts a month, all at one VAT rate.
Downside: every payout needs the fee, each VAT rate and each refund split by hand, and there is no per-order record (customer, products, VAT per line) in FreeAgent.

We wrote it out step by step: How to record Shopify sales in FreeAgent.

Option 2: the FreeAgent PayPal integration (only for PayPal orders)

If your customers pay with PayPal, FreeAgent's article suggests connecting FreeAgent to PayPal and ticking Guess bank transactions, so PayPal fees are split out for you. You then explain the sales income in the PayPal account without invoices. A personal PayPal account cannot connect; you upload statements instead.

Good for: stores where most orders are paid through PayPal.
Downside: it does nothing for Shopify Payments or other card payments.

Option 3: Zapier or Make

Zapier and Make can both connect Shopify and FreeAgent, for example "new paid Shopify order, then create a FreeAgent invoice". You build and maintain the flow yourself.

Good for: people who already use Zapier or Make and want simple invoices.
Downside: your plan limits how many tasks or operations run each month, you have to handle VAT, shipping, discounts and refunds in the flow yourself, and it creates invoices, not the bank explanations that make your FreeAgent bank account balance.

Option 4: Equali

Equali reconciles marketplace payouts (Shopify, Amazon, eBay, Etsy) and posts sales, fees, refunds and taxes into accounting software, including FreeAgent. FreeAgent has a help article on connecting FreeAgent to Equali, which mentions a 14-day free trial and a 20% discount for FreeAgent customers.

Good for: sellers on several marketplaces who want payout reconciliation.
Downside: a broader (and pricier) product than a single Shopify store needs.

Option 5: Bridging Ledger

Bridging Ledger is a UK service built for this exact gap. Its website says it pushes Shopify orders, fees and Shopify Payments payouts into FreeAgent as bank transaction explanations.

Good for: UK sellers who want payout-level bookkeeping.
Downside: check its site for current pricing and how to sign up.

Option 6: Zynk Autopilot

Zynk offers a FreeAgent integration as part of its Autopilot product, covering Shopify, WooCommerce, Wix and eBay orders, refunds and payments. Its page invites you to book a call.

Good for: businesses that sell on several channels and want a managed setup.
Downside: a sales call before you start.

Option 7: Ledgerline (coming soon)

We are building Ledgerline, a Shopify app that sends each paid Shopify order to FreeAgent. It is working against FreeAgent's test environment today and is not on the Shopify App Store yet. When it launches, each paid order becomes:

a FreeAgent contact (matched by email or created), or one shared "Shopify customers" contact if you prefer,
a sales invoice numbered SHOP-(order number) with the same items, the VAT rate Shopify charged on each line, discounts and a shipping line,
marked as sent (FreeAgent does not email your customer), and
a payment recorded in a FreeAgent bank account you choose (for example one called "Shopify"), so the invoice shows as Paid.

Refunds become credit notes marked as refunded. You can preview what will be created before anything is written, and sync orders from the last 60 days. It does not post Shopify fees or payouts yet, and it skips orders in a currency other than your FreeAgent company currency.

Planned pricing: a 14-day free trial, then Basic at USD 9 a month (up to 300 orders a month) or Pro at USD 15 a month (unlimited orders), with yearly options at USD 90 and USD 150.

Which one should you pick?

A few orders a month, one VAT rate: Option 1, by hand.
Mostly PayPal: Option 2.
You want per-order invoices in FreeAgent without building a flow: leave your email below and we will tell you once when Ledgerline is live.
Several marketplaces or payout reconciliation is the priority: Equali or Bridging Ledger.

Notify me at launch

Get one email when Ledgerline is live on the Shopify App Store.

We store your email, the shop URL if you give one, and the time you agreed. We use them to send one email when Ledgerline launches on the Shopify App Store, then delete the list. We send nothing else and share it with no one. To be removed at any time, use the delete link we show after you sign up or email kyle@skillmerc.com.

More Shopify and FreeAgent guides

Ledgerline: Shopify to FreeAgent

Selling on WooCommerce instead?

Our free plugin Skillmerc Sync for FreeAgent sends paid WooCommerce orders to FreeAgent as invoices with VAT, marked as paid. Guides: send WooCommerce orders to FreeAgent and WooCommerce FreeAgent integration options.