Shopify's checkout was built for retail orders, not wholesale buyers asking for net-30 terms or a custom-product customer who wants a deposit on a $4,200 order. For those sales, you need a real invoice: a document that requests payment, lists what's owed, and gives the buyer a way to pay you outside the standard checkout.

Below is a copy-ready template, plus what to include on a Shopify invoice, how Draft Orders work, how to collect ACH payments, and where those payments should land.

Why do Shopify store owners need a dedicated invoicing workflow?

Shopify checkout is good at one job: taking a card payment from a retail buyer who is ready to pay right now. The moment the sale doesn't fit that mold, you're outside what the order confirmation can do.

The usual reasons a Shopify seller needs an invoice:

• Wholesale buyers. A boutique placing a $3,000 reorder expects a PO-matched invoice with net-30 terms, not a Shopify order confirmation email.
• Custom product runs. A 50% deposit upfront, balance on delivery. That's two invoices, not a single checkout.
• B2B customers paying by ACH or wire. Card fees on a $10,000 order eat the margin. Buyers expect to pay by bank transfer.
• Partial payments and milestones. A custom apparel order delivered in two drops bills in two stages.
• Clean records for sales tax and COGS. An invoice is the line-item document your bookkeeper and the IRS expect to see, separate from a payment receipt.

A Shopify order confirmation confirms that an order was placed, while a Shopify invoice requests payment by a specific due date and provides payment instructions. Those are different documents with different jobs.

What should be included on a Shopify store invoice?

Every invoice you send needs to answer four questions: who is billing, who is being billed, what is owed, and how the customer should pay. For a Shopify seller, that breaks down into:

Your business details

• Legal business name and address
• Business tax ID (EIN, or SSN if you're a sole proprietor)
• Store logo (optional but useful for brand recognition)
• Contact email and phone

Invoice identifiers

• Unique invoice number (sequential: INV-1001, INV-1002, etc.)
• Issue date
• Payment due date
• The corresponding Shopify order number, so the invoice reconciles back to a store order

Customer details

• Bill-to name, company, and address
• Ship-to address if different
• Customer PO number if they provided one

Line items

• SKU
• Product name and short description
• Quantity
• Unit price
• Line total

Totals and terms

• Subtotal
• Shipping cost as a separate line
• Discounts as a separate line
• Sales tax as a separate line (don't bury it in the unit price)

• Grand total
• Payment terms (net-15, net-30, deposit required, due on receipt)
• Accepted payment methods

Remittance details

• Bank account for ACH or wire (routing and account number, or a payment link)
• Mailing address if you accept checks
• Late fee policy if you charge one

Where can Shopify store owners get a free invoice template?

Copy the block below into a new document, swap the bracketed fields, and you have a working invoice. It's plain text so it pastes cleanly into Google Docs, Google Sheets, Word, or Excel.

INVOICE

[Your Business Name]
[Street Address]
[City, State ZIP]
[EIN or Tax ID]
[Email] | [Phone]

Invoice #: INV-[0000]
Issue Date: [MM/DD/YYYY]
Due Date: [MM/DD/YYYY]
Shopify Order #: [#1001]
Customer PO #: [if applicable]

BILL TO:
[Customer Business Name]
[Contact Name]
[Street Address]
[City, State ZIP]
[Email]

SHIP TO (if different):
[Address]

------------------------------------------------------------
SKU       | Description       | Qty | Unit Price | Line Total
------------------------------------------------------------
[SKU-001] | [Product name]    |  10 |   $25.00   |  $250.00
[SKU-002] | [Product name]    |   5 |   $40.00   |  $200.00
------------------------------------------------------------

Subtotal:           $450.00
Shipping:            $35.00
Discount:           -$25.00
Sales Tax (8.875%):  $40.84
------------------------------------------------------------
TOTAL DUE:          $500.84

PAYMENT TERMS: Net 30. Payment due by [Due Date].
LATE FEE: 1.5% per month on balances over 30 days past due.

PAYMENT METHODS:
- ACH: Routing [#########], Account [#########]
- Wire: [Bank name, address, routing, account, SWIFT if international]
- Check payable to [Business Name], mail to [address]
- Card payment link: [URL]

Notes:
[Wholesale reorder terms, deposit balance, delivery date, etc.]

Thank you for your order.

Tip: Paste this block into ChatGPT or Claude with the prompt "Turn this invoice template into a fillable Google Sheet with formulas that auto-calculate line totals, subtotal, tax, and grand total, and let me change the tax rate in one cell." You'll get a working spreadsheet (or Excel file, interactive PDF, or Word document if you ask) with the math already wired up. Add your logo and bank details once, then duplicate the file for each new invoice.

How do you send an invoice from Shopify with Draft Orders?

Shopify has a built-in feature called Draft Orders that gets you partway there. You build an order in the admin, then email the customer a checkout link. When they click it, they pay through your store's normal checkout.

The path in Shopify's admin:

1. Go to Orders > Drafts in your Shopify admin
2. Click Create order
3. Add products, set quantities, apply any discounts or custom line items
4. Add the customer (or create a new one)
5. Click Send invoice to email the customer a link to pay

That's useful for one-off custom orders or a quick rebill. But there are real limits:

• Card processing fees still apply. The customer pays through Shopify's checkout, so you pay the same card rate you'd pay on any retail order.
• No native net terms. Draft Orders expect payment at checkout. You can mark an invoice as "payment pending" and reconcile manually, but Shopify isn't tracking the due date or chasing the buyer.
• No native ACH for most merchants. Shopify Payments processes cards. ACH on the invoice means routing the payment through Stripe, a B2B app, or an outside invoicing tool.
• No deposit handling. A 50% deposit / 50% on delivery split isn't a built-in Draft Order flow.

For a single B2B order, Draft Orders work. For recurring wholesale orders or formal net terms, a B2B invoicing app or external invoicing tool usually gives sellers more control.

What invoicing tools work with Shopify?

Most Shopify sellers end up with one of four setups, depending on how much B2B volume they're running:

Shopify Draft Orders. Best for one-off custom orders or occasional wholesale where the buyer is fine paying by card at checkout. No extra tools required.

A B2B or wholesale app from the Shopify App Store. Adds net terms, customer-specific pricing, ACH collection, and recurring billing. Worth it once you're sending more than a handful of B2B invoices a month.

Accounting software (QuickBooks, Xero, Wave). Syncs Shopify orders, generates polished invoice PDFs, tracks aging receivables, and pushes the data straight into your books. Most include a "Pay Invoice" button that accepts ACH or card.

A dedicated invoicing platform. Useful if you're invoicing for custom services on top of products: design work, fulfillment fees, consulting.

Whichever tool prints the PDF, the money has to land somewhere. ACH from a wholesale buyer, a wire from an international customer, the daily Shopify payout: those deposits should consolidate into one business checking account so you can match invoices to incoming funds without bouncing between dashboards.

What business checking features matter for Shopify invoicing?

Novo business checking has a $0 monthly fee, no minimum balance requirement, and Shopify and Stripe integrations, which can fit Shopify sellers that collect most payments online.

What matters for invoicing:

• No monthly fee, no minimum balance. You're not paying a maintenance fee while you wait 30 days for a wholesale invoice to clear.
• No incoming wire fee. Novo does not charge an incoming wire fee, which can matter when wholesale customers pay larger invoices by wire.
• Shopify and Stripe integrations. Shopify checkout payouts and Stripe-collected invoice payments both route to the same Novo account, so reconciliation is one ledger instead of two.
• ACH-ready account details. If your invoicing tool collects ACH, those payments can land in the same Novo account as your Shopify payouts.

A concrete flow: you ship a $4,200 wholesale order on net-30 terms. The buyer pays by ACH on day 28. That $4,200 deposit hits the same Novo account that received this morning's Shopify payout of $1,847 in retail orders. Both deposits show up in the same transaction list, carry the right bookkeeping tags, and reconcile against one monthly statement.

The honest tradeoff: Novo does not accept cash deposits. If you also run a physical pop-up or a brick-and-mortar location taking cash, you'll need a separate solution for that. For Shopify sellers that collect most payments online, the no-cash policy may not affect day-to-day operations.

How should Shopify sellers track invoices for taxes and bookkeeping?

The bookkeeping discipline that pays off at year-end is simple: every invoice ties to a Shopify order ID, every payment ties to a bank deposit, and the documents are all in one place.

A working system:

1. Number invoices sequentially. INV-1001, INV-1002. No gaps, no resets. Sequential invoice numbers create a clearer audit trail for your accountant and make it easier to match invoices to deposits.
2. Save a PDF of every invoice in a dated folder (by month or quarter). Cloud storage is fine.
3. Match the Shopify order number on the invoice so a sale on your store reconciles to the invoice your customer received.
4. Tag the deposit in your bank account with the invoice number when payment arrives. Most accounting software does this automatically when you connect the bank feed.
5. Reconcile monthly, not at year-end.

Common deductions a Shopify seller invoices around:

• Cost of goods sold (COGS): what you paid for the inventory you sold
• Shopify subscription and app fees
• Payment processing fees (Shopify Payments, Stripe, PayPal)
• Shipping supplies and postage
• Marketing spend tied to the products you invoiced

Keep invoiced revenue in a business checking account separate from personal funds. Mixing personal and business funds is a common bookkeeping mistake, and it can make tax reporting harder.

Frequently asked questions

Does Shopify generate invoices automatically?

Shopify sends order confirmations automatically, but those aren't invoices. An invoice asks a customer to pay; a receipt confirms they already did. For an invoice with net terms, a due date, and remittance details, use Draft Orders, a B2B app from the Shopify App Store, or an outside invoicing tool.

Can I invoice a wholesale customer without charging their card immediately?

Yes, but Shopify Draft Orders alone don't support net terms. You'll need a B2B invoicing app from the Shopify App Store or an external invoicing tool to defer payment to net-15, net-30, or net-60.

What's the difference between a Shopify receipt and an invoice?

A receipt confirms a payment that has already happened, whereas an invoice requests a payment that has not yet occurred. Retail Shopify customers get receipts at checkout. Wholesale and B2B customers get invoices first, then a receipt once they pay.

How do I handle sales tax on a Shopify invoice?

Charge sales tax on the invoice the same way Shopify charges it at checkout, based on where you have a tax obligation (nexus) and where the customer is buying from. If you're not sure of the rate, pull it from a recent Shopify order to the same state. Show sales tax as a separate line on the invoice, not buried in the unit price.

Can I collect ACH on a Shopify invoice?

Not through Shopify Payments directly for most merchants. ACH collection on an invoice requires Stripe, a B2B invoicing app from the Shopify App Store, or an outside invoicing platform that can send an ACH payment link.

What payment terms should I offer wholesale customers?

Many wholesale sellers use net-30 terms for established buyers. For custom orders, many sellers require a deposit before production starts. Established repeat customers sometimes get net-60. New customers without trade references typically pay upfront or by card on the first order.

Where should Shopify invoice payments be deposited?

Into a business checking account separate from your personal account, ideally the same one that receives your Shopify payouts. Putting both payment streams into one account, such as a business checking solution like Novo, gives you one ledger for reconciliation instead of two dashboards to cross-reference. If you also sell on other marketplaces, a similar setup helps for Etsy sellers and retail store owners running parallel sales channels.