Guide · B2B

B2B invoice payments with automatic order updates

Published 2026-11-14

Building an app that connects Shopify and QuickBooks lets wholesale buyers order now and pay by bank transfer. The app creates the invoice and marks the Shopify order paid once the invoice is paid in full.

The daily unpaid-orders email from the custom Shopify app, listing bank-transfer orders that are still waiting on payment — See which orders are still waiting for payment.

What you can do

Pay from a bank account

Buyers receive a QuickBooks invoice with a bank payment link.

Order at agreed prices

Buyers review contract pricing and delivery charges before confirming.

Use existing customer records

Invoices go on the customer record your bookkeeper already uses.

See what needs attention

A daily report lists unpaid orders and payment problems.

From confirmed order to paid invoice

An approved buyer chooses invoice payment in the cart. The app creates the unpaid Shopify order and matching QuickBooks invoice, then checks for payment. Staff no longer have to update each order by hand.

What the buyer sees after placing a bank-transfer order, confirming the order and that an invoice was emailed — Buyers receive an order confirmation and an emailed invoice.

What to know

This setup uses Shopify Plus and QuickBooks Online with bank payments enabled.
A voided invoice must not count as payment. The app checks both the invoice balance and total.

Common questions

Does this include net 30 terms?

No. This flow lets buyers pay an invoice after ordering. An agreed due date, such as net 30, is a separate requirement.

What happens to existing invoice numbers?

The app uses your existing QuickBooks numbering sequence rather than a separate prefix. The QuickBooks connector’s invoice sync stays off.

Connect orders, invoices, and payments

Tell me how buyers pay today and which accounting system you use.

Or run a free teardown of your store first.