Automatic invoices for Shopify orders

To issue an automatic invoice for each Shopify order, you need three things: orders that carry complete billing details, one invoice per order and an invoice that reaches the customer as a PDF. VAT rules depend on where the customer is, so set them before you automate anything. These are the steps, in the order to do them.

What you need before you start

• Billing details on the order: name or company name, address and, for business customers, their VAT number.
• A numbering series with no gaps, in a format you can explain to your accountant.
• VAT rules by destination country: what you charge at home, which sales are exempt and which are exports outside the EU.
• One person responsible for reviewing invoices that fail.

Step 1: decide when the invoice is issued

There are two common points: when the order is paid, or when it ships. Pick one and keep it. Invoicing on payment is simpler and avoids invoicing orders that get cancelled. Invoicing on shipment makes sense if paid orders sometimes do not ship.

Step 2: map the tax details

Step 3: apply VAT by destination

As a general rule, the VAT rate depends on where the goods are consumed. For business sales within the EU, reverse charge applies when the customer has a valid VAT number. Sales outside the EU are usually treated as exports. These rules have details and change over time, so confirm them with your adviser and the official sources in your country.

Step 4: keep numbering without gaps

A sequential series is what any review will ask for. If you delete or reissue an invoice, do not change it: issue a credit note instead. Check that numbering does not skip when orders fail.

Step 5: avoid duplicates

Before you switch the automation on, place a test order. Check that:

• It creates one invoice, even if the order is updated afterwards.
• Resending the email does not create another invoice. It only resends the existing one.
• A cancelled order does not leave a valid invoice unreviewed.

Ask your vendor in writing how it handles orders that change after they have been invoiced.

Step 6: send the invoice to the customer

Set up email delivery with the PDF attached. Flowgration can send an order summary and the invoice as a PDF with your logo. Review the email text and contact details before you turn it on.

Step 7: refunds and cancellations

For a refund, issue a credit note that cancels the original amount. Do not edit the original invoice. That keeps the invoice register complete.

Step 8: export for your accountant

Export issued invoices to Excel or CSV each month, so your accountant has them without relying on screenshots. Flowgration does not do accounting or tax filings: the invoice register is exported for your accountant.

Frequently asked questions

Does Shopify issue invoices by itself?

It depends on your setup and the apps you have installed. Before you automate, check what your store already does, so you do not invoice the same order twice.

What if the customer changes their address after paying?

Decide your policy. If invoices are issued on payment, a later change may need a credit note and a new invoice. Confirm with your accountant.

Can I invoice orders from before I connected the tool?

Ask the vendor how it handles earlier orders. Do not assume it does: test with an old order before you load the full history.

How do I handle sales to other EU countries?

Use the customer's VAT details and, for business sales, their VAT number. The rules vary, so confirm them with your adviser.

Do I need a simplified invoice for small orders?

Simplified invoice rules vary by country and amount. Ask your adviser before you decide how to invoice small orders.

For the WooCommerce equivalent, read how to invoice WooCommerce orders. To see how orders connect to the customer record across the store, the CRM for ecommerce page explains it.