If your business runs on Shopify, you’ve probably noticed the gap: Shopify handles product sales well, but invoicing for custom work, services, or non-standard orders requires a workaround. Here are the options that actually work.
Shopify is built for product sales through a checkout flow. When you need to invoice a customer directly—for a custom order, a service, or work outside the standard store transaction—you’re working around the platform rather than with it. Here’s how to handle each scenario.
Option 1: Shopify Draft Orders (for custom products and services)
If you need to charge a customer for something that isn’t a standard product in your store, Draft Orders is Shopify’s built-in solution.
How to create a draft order:
- In your Shopify admin, go to Orders > Drafts
- Click Create Order
- Add products or custom line items with descriptions and prices
- Enter the customer’s information or select an existing customer
- Set a discount or add shipping if needed
- Click Send Invoice to email the customer a payment link
The customer receives an email with a link to complete the purchase through your Shopify checkout. Payment processes normally, and the order appears in your Shopify order history.
When this works well: Custom products with variable pricing, deposit collection, wholesale orders, or anything you’re selling through Shopify’s payment system.
Limitations: The invoice email uses Shopify’s standard template, which is minimal. You can’t send a detailed multi-line service invoice with your logo and custom terms through this method.
Option 2: Shopify Order Printer (for PDF invoices on existing orders)
If you need to generate a printable PDF invoice from a completed order, Shopify’s free Order Printer app or its successor Order Printer Pro handles this.
How to use Order Printer:
- Install Order Printer from the Shopify App Store (it’s free)
- In any order, click More Actions > Print with Order Printer
- Select the invoice template
- Print or save as PDF
Order Printer supports basic template customization—you can add your logo and modify the layout with some HTML knowledge. Order Printer Pro offers more template options and easier customization without code.
When this works well: Generating PDF invoices for completed product orders, providing VAT invoices for business customers, or creating a printable record for accounting purposes.
Option 3: Dedicated invoice apps for Shopify
For more polished, fully customizable invoices tied to Shopify orders, several apps in the Shopify App Store offer this:
Invoice Falcon: Automatically generates branded PDF invoices for every order. Supports multi-currency, VAT, and custom templates. Free tier available with limits; paid plans start around $7/month.
Sufio: Professional invoice generation with B2B features including EU VAT compliance, customer-specific pricing, and bulk invoice creation. Starts around $19/month.
Avada Invoice: Another well-reviewed option with strong template customization and automatic invoice sending on order fulfillment.
These apps integrate directly with your Shopify orders, so invoices generate automatically when orders are placed or fulfilled.
The most common Shopify invoicing mistake is using order confirmations as invoices. Order confirmations are receipts—they confirm a transaction happened. Invoices are formal billing documents that include your business details, tax numbers, and payment terms. For B2B customers who need proper invoices for accounting, the distinction matters.
Option 4: Standalone invoicing tool for service work
If you’re using Shopify for your storefront but also bill clients for services—design work, consulting, custom development, photography—the invoicing for that service work doesn’t need to go through Shopify at all.
A standalone invoicing tool handles service billing cleanly, without the workarounds that Shopify’s order-based system requires. Benefits include:
- Professional branded invoices not tied to an order flow
- Custom line items and descriptions for service work
- Payment terms (Net 30, etc.) rather than immediate checkout
- Invoice tracking (knowing when the client viewed your invoice)
- Integration with your accounting software
For freelancers who happen to sell some products through Shopify but primarily do client service work, a tool purpose-built for that billing context—like Waco3—will produce more professional invoices with less friction.
Which option should you use?
| Situation | Best Option |
|---|---|
| Charging a customer for a custom product | Draft Orders |
| Generating a PDF invoice from a completed order | Order Printer / Invoice app |
| Sending recurring invoices to B2B customers | Invoice app (Sufio, Invoice Falcon) |
| Billing for service work outside of Shopify | Standalone invoicing tool |
| EU VAT compliance | Invoice Falcon or Sufio |
Most Shopify merchants end up using a combination: an invoice app for product order documentation, and a separate tool for any service or consulting billing.
Setting up automatic invoicing for new orders
With any of the Shopify invoice apps, you can configure automatic invoice generation on order completion or fulfillment. Once configured, every new order triggers an invoice PDF automatically—no manual action required.
This is particularly valuable for wholesale or B2B customers who need invoices for every purchase as a matter of their own accounting requirements.
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