Ecommerce Invoices: Shopify, WooCommerce & Amazon Guide

Quick answer: An ecommerce invoice is a formal billing document for an online order, with a unique invoice number, seller and buyer details, line items, tax breakdown and payment status. Consumer orders often only need a receipt, but business buyers, VAT countries and wholesale orders usually need a proper invoice, whether you sell on Shopify, WooCommerce or Amazon.

Online sellers send a lot of documents: order confirmations, shipping notifications, packing slips, receipts and sometimes invoices. Many store owners assume the order confirmation email is an invoice. Sometimes it is close enough; often it is not. The gap usually shows up when a business customer asks for a "proper invoice" for their accounts, a tax authority asks for invoice records, or an accountant tries to match refunds to original sales.

This guide explains when you need an ecommerce invoice, how B2B and B2C requirements differ, how sales tax, VAT and marketplace facilitator rules affect what you put on the invoice, how to number invoices and handle refunds, and when to use an app versus making invoices manually. For one-off invoices, such as a wholesale order or a customer request, you can use our free invoice generator.

Ecommerce invoice vs order confirmation vs receipt

These three documents overlap, which is why they get confused.

Document	Purpose	Typical ecommerce use
Order confirmation	Confirms the order was received	Sent automatically at checkout
Receipt	Proves payment was made	Prepaid consumer orders; often combined with the confirmation
Invoice	Formal bill with legal and tax details	B2B orders, VAT countries, wholesale, on-account terms, customer requests
Packing slip	Lists contents of a shipment, usually without prices	Placed in the box for picking and checking
Commercial invoice	Customs document for cross-border shipments	International orders of physical goods

Because most online orders are paid at checkout, the invoice for an ecommerce sale is often marked "Paid" with a zero balance, which makes it look like a receipt. That is fine. What makes it an invoice is the content: a unique invoice number, your legal and tax details, the date of supply and a proper tax breakdown. Our guide on invoice vs receipt explains the distinction in more depth; a packing slip, by contrast, lists what goes in the box and usually leaves prices off.

B2C vs B2B ecommerce invoices

Consumer (B2C) orders

In the US, consumer sales generally do not require a formal invoice; an emailed receipt showing items, price, tax and payment is normal. In the EU, UK and many other VAT countries, rules are different: some countries require an invoice or simplified invoice for certain consumer sales, and customers can usually request one. If you sell internationally, do not assume US norms apply everywhere.

Business (B2B) orders

Business customers buying through your store, and wholesale buyers ordering by email, usually need a full invoice. They use it to record the expense and, in VAT and GST countries, to reclaim input tax. A B2B ecommerce invoice typically needs:

• Your full legal business name and address, and your tax registration number where you are registered.
• The buyer's company name and address, and their VAT number for cross-border reverse-charge sales in the EU or UK.
• Their PO number if they issued one.
• Payment terms if you are offering credit, such as Net 30 for wholesale accounts.

Retailers buying for resale in the US will often give you a resale certificate so you do not charge sales tax. Keep the certificate on file and note the exemption on the invoice.

Sales tax, VAT and marketplace facilitator rules

Tax is where an ecommerce invoice has to be most precise, and the rules depend on where your customer is, what you sell and which channel the sale goes through.

US sales tax on your own store

When you sell through your own Shopify or WooCommerce store, you are the seller responsible for collecting sales tax in states where you have nexus, which after the 2018 Wayfair decision can include economic nexus from sales volume alone. Your invoice or receipt should show the sales tax charged, ideally by rate or jurisdiction. Our guide to sales tax on US invoices covers what to show, and the sales tax calculator helps you check amounts for manual invoices. The Streamlined Sales Tax Governing Board publishes resources for the states in its agreement.

Marketplace facilitator laws

Every US state with a statewide sales tax, plus Washington, DC, has adopted a marketplace facilitator law; Missouri was the last, with its law taking effect on January 1, 2023. Under these laws, a marketplace that facilitates third-party sales, such as Amazon, Etsy, eBay or Walmart Marketplace, is generally responsible for collecting and remitting sales tax on those sales. As a marketplace seller, that usually means:

• The marketplace calculates and collects tax at checkout on your marketplace orders.
• You should not add sales tax yourself to an invoice for a marketplace order that the marketplace already taxed.
• You may still need to register or file in some states, and sales through your own website are not covered by the marketplace's collection.

Rules differ in detail from state to state, so confirm your obligations with each state's revenue department or a tax professional.

VAT and cross-border sales

If you sell to consumers in the EU, the 2021 e-commerce VAT package changed the rules: VAT is generally charged at the rate of the customer's country once you pass the EU-wide distance-selling threshold, and the One Stop Shop lets sellers report those sales through one return. Marketplaces can be treated as the "deemed supplier" for certain sales, including imported consignments up to EUR 150 and sales by non-EU sellers of goods already in the EU. The European Commission's VAT One Stop Shop portal explains the schemes. For what a compliant VAT invoice must show, see our VAT invoice guide.

Shopify, WooCommerce and Amazon: how invoicing usually works

Platform features change often and vary by plan, region and installed extensions, so treat this as a general orientation and check your own setup.

• Shopify: stores send order confirmation emails that you can customize, and many merchants add an invoicing app from the app store to produce PDF invoices with sequential numbers and tax details. If you sell B2B, check whether your plan and apps support company accounts, payment terms and tax-exempt customers.
• WooCommerce: as an open-source WordPress plugin, it sends order emails out of the box, and PDF invoice generation is typically added through an extension or plugin. Because you control the code and database, you are also responsible for backups and keeping invoice numbering intact through migrations.
• Amazon: invoicing requirements and options depend on the marketplace country and seller programs. Business buyers frequently request invoices, and in some regions sellers are expected to provide them. Check Seller Central help for your marketplace for the current rules on who issues the invoice and how.

Apps vs manual invoices

If most of your orders need invoices, automate with an app or plugin connected to your store. If invoices are occasional, such as a handful of wholesale orders or customer requests each month, creating them manually is simpler and cheaper. Our generator builds a PDF in your browser from the details you enter; it does not connect to your store or import orders, so it fits the occasional-invoice case.

Sample ecommerce invoice for a wholesale order

A boutique retailer orders stock from a ceramics brand that sells through its own Shopify store and directly to wholesale accounts. The retailer has provided a resale certificate and receives a 5% trade discount on goods.

Description	Qty	Unit price	Amount
Stoneware mug, speckled white, 12 oz (SKU MUG-12-WHT)	24	$9.50	$228.00
Teapot, matte black, 1 L (SKU TPT-1L-BLK)	12	$28.00	$336.00
Freight shipping, 2 cartons	1	$35.00	$35.00
Subtotal			$599.00
Trade discount, 5% of goods ($564.00)			-$28.20
Sales tax: exempt, resale certificate on file			$0.00
Total due (Net 30)			$570.80

The arithmetic:

• Mugs: 24 x $9.50 = $228.00.
• Teapots: 12 x $28.00 = $336.00.
• Goods total: $228.00 + $336.00 = $564.00.
• Subtotal including shipping: $564.00 + $35.00 = $599.00.
• Trade discount: $564.00 x 5% = $28.20.
• Total: $599.00 - $28.20 = $570.80.

The discount applies to goods only, not shipping, so the description names its base. SKUs make it easy for the retailer to match the invoice against the delivery. If this were a taxable consumer sale, you would add a sales tax line on the taxable amount, and whether shipping is taxable depends on the state. For a simple product invoice layout, the minimal invoice template keeps SKUs and quantities easy to scan.

Invoice numbering for online stores

Order numbers and invoice numbers are not always the same thing. Order numbers can include abandoned, cancelled or test orders, which leaves gaps. Tax authorities in many countries expect invoice numbers to be unique and sequential, and gaps you cannot explain raise questions in an audit.

• Keep a separate invoice series, such as INV-2026-00001, and assign a number only when an invoice is actually issued.
• Use a prefix per channel, such as WEB-, AMZ- and WHL-, if you invoice several channels from different systems.
• Never reuse numbers, even for cancelled invoices; cancel with a credit note instead.

Our invoice numbering system guide covers formats in detail.

Refunds, returns and credit notes

Ecommerce has a high return rate compared with many other businesses, which makes refund handling a core part of invoicing. When you refund an order that was invoiced, do not edit or delete the original invoice. Issue a credit note that references the original invoice number and shows the returned items, quantities, the tax being reversed and the refund total. For partial refunds, credit only the affected lines.

Credit notes keep your sales tax and VAT reports correct, because the original sale and the reduction are both recorded. Our credit note guide walks through the layout. For marketplace orders, the marketplace typically processes the refund and adjusts the tax it collected, but keep your own records aligned.

What to include on an ecommerce invoice

• Your legal business name, address and contact details.
• Your sales tax, VAT or GST registration number where registered.
• Customer name and billing address; company name and VAT number for B2B.
• Shipping address if different from billing.
• Unique sequential invoice number, plus the order number for reference.
• Invoice date and date of supply or shipment.
• Each product with SKU, quantity, unit price and line total.
• Shipping, discounts and gift cards as separate lines.
• Tax rate and amount, or the exemption or reverse-charge reason.
• Amount paid, payment method and balance due.
• Return policy or a link to it, and payment terms for wholesale accounts.

For international shipments of physical goods, prepare a separate commercial invoice for customs as well.

Common ecommerce invoicing mistakes

• Treating the order email as a tax invoice. It often lacks a sequential invoice number, a tax ID or a proper tax breakdown.
• Charging sales tax twice on marketplace orders. If the marketplace collected tax, do not add it again on an invoice you issue for that order.
• Editing invoices after a refund. Use a credit note so the audit trail stays intact.
• Gaps from cancelled orders. Assign invoice numbers only on issue, from a dedicated series.
• Missing B2B details. A business buyer cannot reclaim VAT without your VAT number and their own on reverse-charge invoices.
• Ignoring exemption paperwork. A tax-exempt wholesale invoice without a valid resale certificate on file can leave you liable for the tax.
• Assuming one country's rules apply everywhere. Cross-border sales bring different VAT, GST and invoice requirements.

Get these basics right and your ecommerce invoices will satisfy business customers, accountants and tax authorities alike, whichever platform your store runs on. For more trade-specific billing guides, browse the industry invoices section.