E-commerce Invoicing: Shopify, WooCommerce, B2B and VAT

E-commerce invoicing is deciding which orders need a formal invoice, producing it with the right tax detail, and keeping invoice numbers and credit notes consistent with your store's order data. For a store selling mostly to consumers, the checkout receipt does most of the work. The effort goes into business buyers, wholesale, cross-border sales and returns, which is where this guide focuses.

The rules below are summarised for the UK, EU and US. They are general information, last reviewed October 2026, not tax advice; check with your tax authority or an adviser for your situation.

When does an online store have to issue an invoice?

The obligation depends on who the buyer is and where you are registered for tax. Three jurisdictions show the range:

United Kingdom. A VAT-registered business must issue a VAT invoice when it makes a standard-rated or reduced-rated supply to another VAT-registered person, and normally within 30 days of the tax point. It does not need to issue VAT invoices to customers who are not VAT registered, though in practice you will issue one to any customer who asks. Retailers can use a less detailed VAT invoice for sales of £250 or less, but must give a full VAT invoice above £250 or when the customer asks (HMRC VAT Notice 700, paragraphs 16.2.1, 16.2.3 and 16.6, accessed October 2026).

European Union. If you are registered for VAT and sell to other businesses, you normally must issue a VAT invoice, on paper or electronically, and your VAT identification number must appear on all invoices you give to customers. For services to a business in another EU country, the invoice shows no VAT because the customer accounts for it under the reverse charge (Your Europe: Charging and deducting VAT). Some countries go further: Belgium's FPS Finance states that from 1 January 2026 all Belgian businesses liable to VAT must use structured electronic invoices with each other (einvoice.belgium.be).

United States. Sales tax rules centre on collecting and reporting the tax rather than on a prescribed invoice format, so the checkout receipt usually serves consumer orders. Business buyers still expect an invoice for their accounts payable, and buyers purchasing for resale or claiming an exemption will give you a certificate that you should keep with the order.

What should an e-commerce invoice show?

An e-commerce invoice needs the standard invoice details plus the order data that online stores handle differently: SKUs, mixed tax rates, shipping and payment status. The UK requirements for a full VAT invoice are a good baseline because they are explicit: a unique sequential number, the tax point, your name, address and VAT number, the customer's name and address, and for each line a description, quantity, VAT rate and net amount, then the totals and the VAT in sterling (HMRC VAT Notice 700, paragraph 16.3.1).

Worked example: a UK business order with two VAT rates. A VAT-registered shop sells to a school: 10 printed books at £12 net (books are 0% in the UK) and 10 tote bags at £8 net (standard rate, 20%), plus £10 delivery. HMRC says an additional charge for delivering goods follows the liability of the goods (VAT Notice 700/24, paragraph 2.2); here the shop splits it by goods value, which is a common approach to agree with your accountant.

Invoice total: £226.80. Charging 20% on the whole £210 would have produced £42.00 of VAT and overcharged the school £25.20. Book rates are listed on HMRC's rates of VAT on different goods and services.

How do Shopify and WooCommerce handle invoices?

Both platforms send order confirmations out of the box; formal invoice PDFs usually need an app or extension, and B2B terms need specific setup.

Shopify. Shopify's help centre points merchants to the Shopify Order Printer app to "print and customize invoices, packing slips, pick lists, and other documents", with templates editable in HTML, CSS and Liquid (Shopify Help: Order Printer). For B2B, Shopify supports payment terms of Net 7, 15, 30, 45, 60 and 90 days (starting from the day the order is placed), due on fulfillment, or a fixed date on individual draft orders; deposit requirements are available only on Shopify Plus (Shopify Help: Payment terms, accessed October 2026).

WooCommerce. For orders in Draft or Pending payment status, WooCommerce lets you choose Order actions, then "Send order details to customer", which emails the customer an invoice with a payment link; you can also share the order's customer payment page link (WooCommerce: Paying for orders). The documentation does not describe PDF tax invoices, so stores that need them typically add an extension. Before choosing one, check that it numbers invoices in their own sequence, shows VAT per line and creates credit notes.

Whichever app you use, test three orders before relying on it: a mixed-rate order, a discounted order and a partial refund. Compare the PDF with what your accountant expects.

How should invoice numbers work in an online store?

Give invoices their own unique sequential series and generate the number only when the invoice is issued, not when the order is created. Store order numbers count every checkout attempt your platform records, including orders that are later cancelled, so using them as invoice numbers produces gaps that are hard to explain.

Practical rules:

• One series per legal entity. If you run two stores under one company, either share one series or give each a prefix (for example UK-2026-0001 and EU-2026-0001), and document it.
• Credit notes in their own series (for example CN-0001), each referencing the invoice it corrects.
• Never reuse a number, even for a cancelled invoice. Cancel it with a credit note instead.
• Record the order number on the invoice so support and finance can match them.

The invoice number generator shows common formats, and the record-keeping guide covers how long to keep invoices.

How should returns and refunds be documented?

Issue a credit note that references the original invoice; do not edit or delete the invoice. In the UK, a valid credit note must show its own identifying number and date, the supplier's and customer's details, the amounts and VAT credited, and the number and date of the original invoice, and it should reflect a genuine mistake, overcharge or agreed reduction (HMRC VAT Notice 700, paragraph 18.2.3).

For mixed-rate orders, credit each line at the rate it was invoiced at. A credit note that reverses VAT at a single rate will not match the original invoice. See credit notes explained for the general rules.

Who issues the invoice on Amazon, Etsy and other marketplaces?

On marketplaces, the marketplace usually records the order and, in many US states, collects the sales tax as the "marketplace facilitator". California's tax agency, for example, explains that from 1 October 2019 a seller may not be responsible for sales or use tax on sales made through a registered marketplace facilitator, but must still report those sales and claim them as a deduction (CDTFA Publication L-700).

You may still need to issue your own invoice when a business buyer asks for one, and you need to reconcile marketplace payouts against orders, fees and refunds in your books. Keep the marketplace's settlement reports with your records. If the marketplace collected the tax, your invoice should not charge it a second time.

What changes for wholesale and B2B orders?

Wholesale is where an online store starts to look like a service business: orders are larger, buyers pay on terms, and their accounts payable team needs a complete invoice before paying.

Worked example: a wholesale order on Net 30. A boutique orders 120 candles at $14 wholesale. The invoice shows: buyer's legal name and billing address, their purchase order number, 120 × $14 = $1,680, shipping $45, resale certificate on file (no sales tax charged), total $1,725, due 30 days from the invoice date, with bank transfer details and a card payment link. If the boutique pays $1,000 first, the invoice stays open for the remaining $725, and your reminders should ask for that balance only.

Set up wholesale separately from consumer checkout: a wholesale price list, a customer record with tax status and terms, and invoices issued from your platform's B2B features or a separate invoicing tool. The payment terms guide explains Net terms, deposits and early-payment discounts, and the late payment guide covers follow-up.

Where does InvoiceQuickly fit for an online store?

InvoiceQuickly does not connect to Shopify, WooCommerce, Amazon or Etsy, and it does not create invoices from store orders. It is not a good fit for per-order invoicing.

It can fit the occasional wholesale or B2B invoice that sits outside your store, like the candle example above. You type or say what to bill, review the draft and save it. On Pro ($9/month) you can email it with a PDF, add a payment link from your own Stripe or PayPal account for the remaining balance, record partial payments, send scheduled reminders before and after the due date, and issue credit notes against an invoice.

Two limits matter for e-commerce in particular:

• One tax rate per invoice. InvoiceQuickly applies a single tax percentage to the discounted subtotal. It cannot show the mixed-rate invoice in the UK example above, or per-line VAT.
• PDF only, English only. It stores your tax ID and copies it to new invoice PDFs, and it has no structured e-invoice formats such as Peppol, so it does not meet Belgium's B2B requirement.

The features page lists everything by plan, and regional invoicing resources explain country rules in more detail.

Frequently asked questions

Do I need to send an invoice for every online order?

Usually not for consumer orders paid at checkout; an order confirmation and receipt are enough in most cases. Business buyers, wholesale orders on terms and customers who ask for a VAT invoice need a proper invoice. In the UK, retailers must provide a full VAT invoice for sales over £250 or whenever a customer asks.

Is an order confirmation the same as an invoice?

No. An order confirmation records what was ordered. An invoice requests or records payment and, for tax purposes, must carry specific details such as a unique sequential number, your tax registration number, and the tax rate and amount. Many stores send a receipt that covers consumer needs but would not satisfy a business buyer reclaiming VAT.

Does Shopify create invoices automatically?

Shopify sends order confirmations by default. Its help centre directs merchants to the Shopify Order Printer app to print and customise invoices and packing slips. B2B orders can carry payment terms such as Net 30, and draft orders can be sent to customers as invoices requesting payment.

How do I show different VAT rates on one invoice?

List each item with its own VAT rate and net amount, and total the VAT for each rate. Delivery charges follow the VAT treatment of the goods delivered, so on a mixed-rate order they are usually split between the rates. Check the split method with your accountant.

What is the difference between e-commerce invoicing and e-invoicing?

E-commerce invoicing means invoices issued by an online store, which are often PDFs or emails. E-invoicing means structured electronic invoices in a machine-readable format, sent through a network such as Peppol and, in some countries, required by law for B2B sales. A store can need both: PDFs for consumers and structured e-invoices for business buyers in a mandated country.

Who invoices the customer on Amazon or Etsy?

The marketplace records the order and, in many US states, collects sales tax as the marketplace facilitator. You remain the seller and may need to provide an invoice if a business buyer asks, without charging tax that the marketplace already collected.