Shopify Order Invoice Email: Fix the Invoice Number

The problem

A merchant asked about this on the Shopify Community, and it is a genuinely confusing one for anyone selling business to business.

They run a made to order B2B store. Customers are on payment terms, so they do not pay when they order. They pay on dispatch. The merchant sends a payment request at that point.

Here is the clash. For a single order, Shopify produced two things that both call themselves an "invoice", each with a different number.

When the order is placed, Shopify auto-generates a VAT invoice with its own sequential number, something like INV-GB-138. That is the document the customer sees in their account.

Then, when the merchant clicks Send invoice (or Resend invoice) to request payment, the email that goes out is labelled Invoice #1143. But 1143 is the order number, not an invoice number. That label shows in both the email subject and the email body.

So the customer gets one email referencing "Invoice 1143" and sees another document in their account referencing "INV-GB-138", for the same order. It looks like two separate invoices with two separate numbers.

The Shopify Order invoice email today, where the subject and heading both show the order number, not the VAT number

I reproduced this on a test store and confirmed exactly where every number comes from. The good news is that the email is fully editable, and the fix takes about a minute.

Why the email says "Invoice #1143"

Let me explain the mechanism, because it tells you why you cannot simply swap in the VAT number.

Shopify has two separate systems here, and they do not talk to each other.

The first is the native VAT invoice. Shopify generates this automatically at order placement for stores in regions that require it, and gives it a sequential tax number like INV-GB-138. This is the real tax document, and it is the one shown to the customer in their account.

The second is the Order invoice email. This is a customer notification. It is the email your Send invoice and Resend invoice buttons send, and its whole job is to give the customer a "pay now" link for an order with an outstanding balance.

That email is built from a template. And in the default template, the word "Invoice" is followed by the order number, not the VAT number. Two spots do this:

The subject is Invoice {{name}}. The {{name}} variable prints the order name, so it renders "Invoice #1143".

The body heading is Invoice {{ order_name }}. Same idea, {{ order_name }} is the order name, so the big heading at the top of the email renders "INVOICE #1143".

Nothing is broken. The email is simply using your order number and calling it an invoice. That is what creates the appearance of a second, differently numbered invoice.

It is theme text you can edit, not a fixed template

One of the merchant's questions was whether the payment request email is editable at all, or whether it is locked.

It is editable. Both the subject and the full HTML body can be changed. It lives in your store settings, not in any app, and you do not need code skills beyond finding and changing a couple of words.

Here is where it is. Go to Settings, then Notifications, then Customer notifications. Scroll to the Order exceptions group and open Order invoice. Its description reads "Sent when an order has an outstanding balance", which is exactly the payment terms situation.

The Order invoice notification under Order exceptions in Shopify customer notifications

Open it, then click Edit code. That gives you the email subject field and the HTML body.

The fix: rename it from Invoice to Payment request

The cleanest fix is to stop calling this email an invoice at all. Then it no longer competes with your VAT invoice, and the two documents each have one clear job.

You will change two things.

Email subject. Change Invoice {{name}} to Payment request for order {{name}}. Keep the {{name}} variable so the order number still appears.

Email body. In the body code, find the heading line Invoice {{ order_name }}. It is the big "INVOICE #..." near the top of the email. Change the word Invoice to Payment request. Keep {{ order_name }} in place.

The two edits in the Order invoice template, the subject field and the body heading

Save, then use Preview or Send test to check it. The email will now read "Payment request for order #1143" in the subject and "Payment request #1143" as the heading.

Keep the order number in there. It is the reference the customer quotes when they pay, and it is how your own team matches the payment back to the order. You are not removing the number. You are only removing the word "Invoice" so the email stops posing as a tax invoice.

Can I put the VAT invoice number (INV-GB-138) in the email instead?

This was the merchant's main hope: align the payment email with the actual VAT number so both documents match.

The short answer is no, and it is worth knowing why so you do not spend time hunting for a setting that does not exist.

The Order invoice email exposes a fixed set of Liquid variables, and they cover the order: its name, its line items, its totals, the customer, the payment terms. The VAT invoice number is not one of them. There is no variable that prints INV-GB-138 in this email, so there is no way to auto-insert it.

That is the reason the recommended fix is to relabel the email rather than renumber it. You cannot make the payment request carry the VAT number, but you can make it stop claiming to be an invoice. Once it is a "payment request", the number mismatch stops mattering, because only one of the two documents is now an invoice.

The recommended B2B setup

Putting it together, here is a clean setup for a store that invoices on dispatch under payment terms.

Treat the native VAT invoice as your single tax invoice. INV-GB-138 is the customer-facing tax document in their account, and it is the one your accountant works from. Let it be the only thing called an invoice.

Use the relabelled Order invoice email purely as the pay-now request. After the rename above, it is a payment request that links to checkout for the outstanding balance. It references the order number so everyone can match it.

Lean on native B2B payment terms. The "Due on fulfillment" term matches a dispatch trigger nicely, since the balance becomes due exactly when you fulfil. Shopify also has a Payment reminder notification, described as "Sent on or after the due date for an unpaid order", which covers anything overdue without you chasing it manually.

The net result is one number the customer sees on the payment request, which is the order number, and one invoice number, which is the VAT number. No more two-invoices confusion.

One thing worth a quick word with your accountant: Shopify generates that VAT invoice at order placement, not at dispatch. If your tax point is dispatch, confirm that the placement-time invoice still matches what you are required to issue.

Can I change the Shopify invoice number itself?

People often reach this problem while trying to change "the invoice number" directly, so it helps to separate what is and is not editable.

The VAT invoice number (INV-GB-138) is generated by Shopify and is not freely editable. It is sequential by design, because tax invoices are meant to be.

The order number (#1143) can be styled a little. Under Settings, then General, you can set an order ID prefix and suffix, for example turning #1143 into "INV-1143" or "1143-EU". You cannot set the starting number or the increment, and you cannot make it non-sequential.

So if your goal was really "make the payment email use a proper invoice number", the honest position is that Shopify does not let you renumber the payment email to match the VAT invoice. Relabelling it, as above, is the supported way to remove the confusion.

Order invoice, Draft order invoice, and VAT invoice: the three documents

A lot of the confusion here comes from three different Shopify things sharing the word "invoice". Sorting them out helps.

Order invoice is the customer notification this article is about. It is the payment request email for a live order that has an outstanding balance. Editable under Settings, Notifications, Customer notifications.

Draft order invoice is a separate notification, sent when you create an invoice from the draft orders page, before the order is a real order. It is a different template with its own text, so do not edit this one expecting the payment email to change.

VAT invoice (or tax invoice) is the compliant PDF Shopify auto-generates for the order. It carries the INV-GB-138 style number and is the actual tax document. It is not a notification template and is not edited in the same place.

When something looks wrong, decide which of the three you are actually looking at first. It points you straight at the right screen.

What to check if the email still says Invoice

If you renamed it and a test still shows "Invoice", run through these.

You edited a different notification. Make sure you were in Order invoice under Order exceptions, not Draft order invoice under Order processing.

You changed only one of the two spots. Both the subject and the body heading carry the label. Change both.

You are looking at the VAT PDF, not the email. The PDF in the customer account still says invoice, correctly, because it is the invoice. Only the email needed relabelling.

You saved but tested an old email. Re-send a fresh test after saving, since a previously sent email keeps its old wording.

Prefer a proper branded invoice instead?

If your goal is not just to remove the clash but to hand customers a branded PDF invoice with your own sequential numbering, that is an app job rather than a settings change.

Invoicing apps like Sufio, Order Printer Pro, and F+2: Invoices generate branded PDF invoices with configurable numbering, and can attach or email them automatically. They sit alongside the native VAT invoice rather than replacing it, and they give you the control over invoice numbering that the built-in email does not.

For a store that just needs the payment email to stop calling itself an invoice, though, the two-word rename above is all it takes, and it is free.

The short version

Shopify's Send invoice email is the Order invoice notification. It labels itself "Invoice #1143" because it prints your order number, not the native VAT invoice number, and there is no variable to swap the VAT number in.

Open Settings, Notifications, Customer notifications, Order invoice, Edit code. Change the subject from Invoice {{name}} to Payment request for order {{name}}, and change the body heading Invoice {{ order_name }} to Payment request {{ order_name }}. Save.

I reproduced this on a store running the native Order invoice template, and confirmed the default subject Invoice {{name}} and body heading Invoice {{ order_name }} are both editable, with no VAT-invoice-number variable available in that email.