How to create an invoice on Shopify with draft orders

The short version: To create an invoice in Shopify, create a draft order and send the checkout link. That link is the invoice: it carries the line items, taxes, total and payment terms, so the customer pays without leaving your store. Once paid, the draft order becomes the order, so you do not create a separate invoice afterwards. Shopify's 2025 invoice guide identifies 11 must-have parts of a professional invoice, and the draft-order checkout covers most of them natively. If you need a PDF, a specific layout or a credit note, an app belongs in your workflow. Draft orders created on or after 1 April 2025 are automatically deleted after one year of inactivity, according to Shopify's own documentation.

Most people searching for how to create an invoice on Shopify expect a button labelled Invoice. There is no such button.

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The admin has Orders, and inside Orders there is a Create order screen. That is where the work happens. If you are setting up from scratch, our Shopify Switzerland: set up your store guide walks through the admin. If you are still evaluating the platform, what is Shopify and does it work in Switzerland covers the basics.

This article assumes the store exists and you need to bill a customer outside the normal online checkout. A wholesale order, a phone sale, a custom commission. All need an invoice. All start as a draft.

Your invoice is a draft order

The thesis in one line. In Shopify, an invoice is not a document you produce. It is a draft order waiting for payment.

That reframing matters because every other question has an obvious home once you stop looking for an invoice button. The draft order carries the line items. It carries the tax. It carries the customer's name and address. When you send it, Shopify generates a secure checkout link, and that link is what the customer receives.

Shopify's 2025 invoice guide identifies 11 must-have parts of a professional invoice.

These include the word "invoice," a unique number, dates, seller and buyer details, line items, totals, taxes, payment terms, a payment link, accepted methods, and notes. The draft-order checkout covers most of these without extra configuration.

The gap is the PDF. A checkout link is a web page, not a document your accountant can file. That distinction, link versus document, is the whole story of when the native workflow is enough and when an app enters the picture.

Build the order before you send anything

The draft order is where you assemble everything the invoice will show. Open Orders in the admin, click Create order, and the screen gives you the building blocks.

Here is the core sequence:

1. Add products by searching your catalog or entering a custom item with its own price.
2. Adjust quantities and unit prices, or apply a discount as a percentage or fixed amount.
3. Select or create the customer. Their name, address and contact details populate the invoice automatically.
4. Set the shipping address and method. Shopify calculates shipping if you have rates configured.
5. Add internal notes (visible only to staff) and a customer note (visible on the order).
6. Review the tax calculation, which Shopify applies based on your settings and the customer's region.
7. Save the draft. Shopify assigns a draft order number, which becomes the invoice number once the order is paid.

The draft order number is your invoice number. Shopify formats it as #D followed by a sequence, for example #D1024. You cannot change the format natively, though apps can override it. If you need a specific numbering scheme for Swiss accounting, that is already a sign an app belongs in your workflow.

Custom prices matter here. A wholesale buyer wants CHF 42 per unit instead of the retail CHF 59? You edit the line price directly. A surcharge for rush delivery? Add it as a custom item. The draft order does not enforce your storefront pricing, so you control what the invoice says.

Where MWST/TVA sits on the invoice

Tax on a draft order is a settings question before it is an invoice question. Shopify calculates MWST/TVA automatically once you have configured tax rates and regions in Settings. If you have not done that, the draft order will show CHF 0.00 tax regardless of what the customer owes.

For a domestic sale, your store in Switzerland and buyer in Switzerland, Shopify applies the standard rate to taxable goods. The draft order shows it as a line below the subtotal. The buyer sees it on the checkout page. That is your invoice's tax line.

Cross-border is where it shifts. Sell to a customer in Germany, and the parcel leaves the Swiss customs border. The sale is an export. Whether you charge MWST on that sale depends on where the goods are consumed and whether you are registered for VAT in the destination country. Our guide on how to charge MWST on your Shopify store covers the registration threshold. This is CHF 100,000 of worldwide annual turnover per the Federal Tax Administration (ESTV/AFC). It also covers the settings that follow.

The draft order inherits whatever your tax settings produce. If the settings are wrong, the invoice is wrong. Fix the settings, not the invoice.

For Swiss sellers watching the EU, the regulatory clock is ticking. The EU's ViDA package was formally adopted in March 2025. It will be phased in gradually through 2035, according to the European Commission's Directorate-General for Taxation and Customs Union. From 1 July 2030, cross-border B2B transactions in the EU will face mandatory e-invoicing under new Digital Reporting Requirements. By 1 January 2035, EU Member States with domestic digital real-time reporting obligations must align their systems with the cross-border system, the same Commission source states. A checkout link may not satisfy that framework forever.

Send it: the checkout link is the invoice

Once the draft order is saved, the Send invoice action appears. Click it, and Shopify emails the customer a secure checkout link. That link is the invoice.

The email Shopify sends is plain. It includes the store name, the order summary, and a button that takes the buyer to the checkout page. On that page, the buyer sees every line item, the tax, the total and the available payment methods. They pay there. The order converts from draft to paid.

Payment methods at the checkout depend on what you have activated. If Shopify Payments is on, the buyer sees card payment. If you have added TWINT at your Shopify checkout, the buyer sees TWINT. This matters more than it sounds. 77% of online shoppers will abandon a purchase if their preferred payment option is unavailable, according to Shopify's 2025 invoice guide. For a Swiss buyer, that preferred option is often TWINT. If you process cards through a Swiss acquirer, Worldline and Shopify covers how the incumbent option fits.

You can add a custom message to the invoice email. Shopify's default text is functional but generic. Here is a suggested message you can paste into the email:

Payment due within 30 days of the invoice date. Please use the checkout link above to pay by card or TWINT. Questions? Reply to this email.

Payment terms are not a native field. There is no due-date picker on the draft order. You state the terms in the customer note or the email message, and the buyer pays, or does not, within that window.

Re-sending the same link is your reminder system. The checkout link does not expire as long as the draft order is active. Send it again, and the buyer gets the same page with the same total. No app required.

After payment: no second invoice needed

This is where most confusion sits. The buyer pays. The draft order becomes an order. Do you now create an invoice?

No. The order is the invoice. It has the same number minus the D prefix, the same line items, the same tax, the same total. The order confirmation email Shopify sends to the buyer is the receipt. The order record in your admin is the document your accountant works from.

If the buyer does not pay, the draft order stays open. You can cancel it, which removes it from your active orders. Or you leave it, and Shopify handles the cleanup. Draft orders created on or after 1 April 2025 are automatically deleted after one year of inactivity, according to Shopify's documentation. Any edit resets that timer.

Refunds are a different flow. A paid order can be refunded from the order screen. You issue a partial or full refund, and Shopify records it against the order. But a refund is not a credit note. A credit note is a separate document with its own number, referencing the original invoice. Shopify does not generate credit notes natively. If your Swiss accountant expects a Gutschrift with a sequential number, you need an app or you create one outside Shopify.

An invoice is also not a receipt. The invoice requests payment; the receipt confirms it. In the draft-order workflow, the checkout link is the request and the order confirmation is the receipt. One document before payment, one after.

When you need more than a checkout link

The native workflow covers most B2C and simple B2B billing. It breaks down at four points: you need a PDF, you need a credit note, you need recurring invoices, or you need control over the invoice number format.

The e-invoicing market is moving fast. The global e-invoicing market reached USD 15.9 billion in 2024 and will hit USD 68.7 billion by 2033, according to Shopify's 2025 invoice guide. Businesses were projected to generate about 560 billion invoices that year. However, only 125 billion, 22%, were transmitted electronically, per a May 2024 Peppol report cited in the same source. Full global adoption could unlock USD 616 billion in economic gains, with 83% flowing to small businesses, according to an Avalara and Cebr study. A PDF is the minimum a Swiss accountant will want to file.

Here is how the native workflow compares with three apps from the Shopify App Store:

App pricing changes frequently and varies by plan tier. The App Store listing for each tool is the authoritative source for current monthly costs. For context on what your Shopify plan itself costs, see Shopify Preise: what a Swiss shop really pays and what Shopify costs in Switzerland. Current plan rates are on Shopify's Swiss pricing page, checked on 26 August 2026.

Our take: For a Swiss store doing occasional wholesale or custom orders, the native draft order is enough. The checkout link is the invoice, and the order confirmation is the receipt. Pay for an app when your accountant asks for a PDF, when you issue credit notes regularly, or when you invoice the same customer every month. Until one of those three things is true, the native workflow saves you the subscription.

France's phased e-invoicing rollout starts in September 2026 for large enterprises. By September 2027, all businesses in France must issue and receive e-invoices, according to the same Shopify guide. Switzerland has no equivalent mandate today. But if you sell into the EU, the direction is clear: structured invoice data is coming.

Frequently asked questions

Can I send an invoice for an order that has already been paid in Shopify?

A paid order already has a confirmation email and an order record. That is the invoice and the receipt together. You can resend the order confirmation from the order screen, but creating a new draft order for a paid sale duplicates the record and the number. If the buyer needs a branded PDF of the paid order, that is where an app like Sufio or Vify earns its place.

How do I edit or cancel a Shopify invoice after it has been sent?

Open the draft order in your admin and edit any field: line items, prices, customer details. The checkout link the buyer received updates automatically because it points to the live draft, not a snapshot. To cancel entirely, click More actions and select Delete. The buyer's link stops working immediately. If the order has already been paid, you cannot edit the draft. You refund from the order screen instead.

How do I issue a credit note or refund invoice on Shopify?

Refunds happen on the order screen. You enter the amount and Shopify records it against the original order. A credit note, a Gutschrift with its own sequential number, is different. Shopify does not generate one natively. You need an invoicing app such as Sufio, Invoicify or Vify, or you create the document in your accounting software and reference the Shopify order number manually.

Does creating a draft order invoice reserve inventory before the customer pays?

No. A draft order does not reserve or reduce stock. Inventory is deducted only when the draft becomes a paid order and you mark it as fulfilled. This matters for wholesale: if you invoice a customer for 50 units and only 40 are in stock, the draft order does not warn you. Check stock manually before sending the invoice.

How do I set up recurring invoices natively in Shopify?

You cannot. Shopify's draft orders are one-off documents with no scheduling, no automatic repeat, and no native subscription billing cycle. For recurring invoices, a monthly retainer or a service contract, you need either a subscription app or an invoicing app with recurring features. Vify and Sufio both offer recurring invoice scheduling on their paid plans.

Can I add my logo to the default Shopify draft order invoice?

Not to the checkout link itself. That page uses your store's checkout branding, which includes your logo if you have uploaded one in Settings. The invoice email Shopify sends is plain text with no logo and no custom layout. To send a branded PDF with your logo, colours and typography, you need an invoicing app. The native workflow does not produce a PDF at all.

Sources

1. Shopify Inc., "Draft orders and invoices". https://help.shopify.com/en/manual/fulfillment/managing-orders/create-orders — checked on 26 August 2026.
2. Shopify Inc., "Sending invoices for draft orders". https://help.shopify.com/en/manual/fulfillment/managing-orders/create-orders/send-draft — checked on 26 August 2026.
3. Shopify Inc., "What Is an Invoice? Definition, Types & How to Create Invoices (2026)". https://www.shopify.com/blog/retail-invoice-guide — checked on 26 August 2026.
4. European Commission, Directorate-General for Taxation and Customs Union, "VAT in the Digital Age: 2026 Work Programme available". https://taxation-customs.ec.europa.eu/news/vat-digital-age-2026-work-programme-available-2026-05-22_en — checked on 26 August 2026.
5. European Commission, "ViDA implementation Work programme". https://taxation-customs.ec.europa.eu/document/download/c6153542-8b34-4308-b7e4-9e65e55eb79d_en?filename=ViDA+implementation-Work+program.pdf — checked on 26 August 2026.