Knowledge Base Getting Started Frequently Asked Questions

How to use Shopify with FreeAgent

This article explains the different ways you can use Shopify in FreeAgent.

If you haven’t already set up your Shopify integration with FreeAgent, check out this article.

Sales and refunds from Shopify

Every night, one invoice and one credit note will be automatically created in FreeAgent, containing the total amount of all the orders you received into your Shopify store for the previous 24-hour period. Sales will appear on the invoice, and any refunds will appear on the credit note. If there have been no sales or refunds during that period, nothing new will be created.

Your orders are grouped together by VAT rate, with different VAT rates appearing as individual line items. The contact for every invoice and credit note will be listed as Shopify.

Here’s an example of an invoice imported by the Shopify integration.


Below is an example of a credit note imported by the Shopify integration.


How to use the Shopify bank account in FreeAgent

Money for orders

Every time you receive a payment for an order in your Shopify account, FreeAgent will create a transaction in your Shopify bank account.

This will automatically be explained as ‘Invoice Receipt’ against the invoice that contains the order linked to the payment received.


If you refund a payment for a cancelled order in your Shopify account, FreeAgent will also create this transaction in your Shopify bank account.

This transaction will automatically be explained as ‘Credit Note Refund’, and link to the relevant credit note.



You will occasionally incur Shopify fees, such as your Shopify subscription billing, transactional fees or third-party payment provider fees.

Any fees incurred over the previous 24-hour period will be pushed into your Shopify bank account in FreeAgent as one “money out” transaction. The category this transaction is explained to will match the category chosen in your initial Shopify configuration stage.



When you import a Shopify payout transaction into your bank account (by bank feed or uploading a statement), you’ll then need to explain this as a transfer from the Shopify bank account.

Reconciling unpaid orders

If you receive an order that is never paid for, and then gets cancelled - this outstanding order will be reflected on both an invoice (for the order) and a credit note (for the cancelled order) within FreeAgent.

If this happens, you’ll then need to follow our guide to net off a sales invoice and credit note for the amount of this order.

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