How to Accept Payments on QuickBooks Invoices (Without Switching Provider)

You've sent the invoice. It's sitting in your customer's inbox. And now you wait, 30 days, 45 days, sometimes longer, for a cheque, a bank transfer, or a phone call asking for your bank details.

QuickBooks makes invoicing easy. Collecting is the problem.

This guide walks through how to add online payment capability to your QuickBooks invoices so customers can pay by card, PayPal, Apple Pay, or Google Pay, directly from the invoice. And critically, how to do it while keeping a supported gateway you already use. To collect bank payments specifically, see How to Accept ACH Payments in QuickBooks.

The QuickBooks Payment Collection Problem

QuickBooks Online is used by millions of small and mid-sized businesses globally. The invoicing feature is mature: recurring invoices, customisation, automated reminders. But when it comes to actually getting paid, businesses hit a wall:

• QuickBooks Payments (Intuit's own processor) works natively but locks you into their rates and is only available in the US

• Third-party gateways you already use (Authorize.net, Stripe, Worldpay, Braintree) don't connect to QuickBooks invoices natively

• Manual reconciliation is the default: payments come in via one system, invoices live in another, and someone has to match them

The result: invoices go out fast, payments come back slow, and finance teams spend hours reconciling.

Option 1: QuickBooks Payments (Intuit Native)

Intuit's own payment processor integrates directly with QuickBooks Online. Customers see a "Pay Now" button on invoices.

Pros:

• Native integration: no setup required beyond enabling

• Auto-reconciliation built in

Limitations:

• US only

• Intuit sets the processing rates (2.99% card, 1% ACH)

• You can't use your existing gateway: it's Intuit or nothing

• No multi-PSP support: if you process through Stripe, Worldpay, or Authorize.net elsewhere, you now have two payment stacks to manage

• Limited payment methods compared to specialist gateways

For US-only businesses with simple payment needs and no existing gateway relationship, QuickBooks Payments works. For everyone else, there's a gap.

Option 2: Add Payment Links to QuickBooks Invoices

The alternative: connect a supported gateway you already use to QuickBooks and add a payment link to every invoice. Customers click, pay, and the payment is recorded back into QuickBooks automatically.

This is what Shuttle's QuickBooks Online Invoice Payments app does:

1. Connect your gateway: Authorize.net, Braintree, PayPal, Stripe, Worldpay Access, and more

2. Get a payment link: a unique URL tied to your QuickBooks account

3. Paste into invoices: add the link to your invoice template or individual invoices

4. Customer pays: they click, enter card details (or use Apple Pay / Google Pay), and pay

5. Auto-recorded: the payment is automatically recorded back into QuickBooks, matched to the invoice

No migration. No switching processors. Your existing gateway rates, settlement, and merchant account stay exactly as they are.

Why This Matters for Your Business

Keep your negotiated rates. If you've spent years building a relationship with your payment provider and negotiating processing rates, you shouldn't have to abandon that just to add a pay button to invoices.

One payment stack. Instead of running QuickBooks Payments alongside your existing gateway, everything processes through the same provider. One set of reports, one relationship.

Works internationally. QuickBooks Payments is US-only. If you invoice customers in the UK, EU, Australia, or anywhere else, you need a gateway that supports those regions. Shuttle connects supported international gateways to QuickBooks.

Payment methods. Depending on your gateway, customers can pay by card, PayPal, Apple Pay and Google Pay.

How to Set It Up

To set up online invoice payments in QuickBooks via Shuttle:

Step 1: Install the App

Go to the QuickBooks Online Invoice Payments app and click "Get App." Connect your QuickBooks Online account via OAuth: standard QuickBooks app authorisation.

Step 2: Connect Your Payment Gateway

Choose from the supported gateways:

• Authorize.net: full integration guide

• Stripe: if you already process cards through Stripe

• Braintree: PayPal's gateway for card processing

• PayPal: direct PayPal payments

• Worldpay Access: for UK and international merchants

• USAePay: US-focused gateway

Enter your gateway credentials or connect via OAuth. Your existing merchant account and rates remain unchanged.

Step 3: Configure Settings

Choose which features to enable:

• Saved cards: customers can save card details for faster future payments

• Partial payments: accept deposits or instalments against invoices

• Email notifications: get alerted when a payment is made

• Custom branding (Basic plan): your logo and custom payment URL

Step 4: Add the Link to Invoices

Copy your unique payment link and paste it into your QuickBooks invoice template. Every invoice you send will now include a "Pay Online" option.

Alternatively, add the link to specific invoices only, useful if some customers prefer bank transfer.

What Your Customer Sees

When a customer receives your invoice with the payment link:

1. They click the link

2. A branded checkout page opens (your logo on the Basic plan)

3. They enter card details or choose Apple Pay / Google Pay

4. Payment is processed through your gateway

5. They see a confirmation

6. The payment is auto-recorded in QuickBooks against the correct invoice

No account creation. No app download. Just click and pay.

Auto-Recorded Payments: The Real Time Saver

The biggest operational win isn't the faster payment. It's that each payment is recorded against its invoice in QuickBooks.

Every payment processed through the link is recorded back into QuickBooks against the correct invoice. The invoice status updates to "Paid" (or partially paid). Your books stay accurate without anyone manually marking invoices as paid.

For businesses sending 50+ invoices per month, this cuts manual matching work.

Pricing

Free plan: Auto-record payments, saved cards, partial payments, email notifications, PCI DSS Level 1 compliance. No transaction fee from Shuttle (your normal gateway fees apply).

Basic plan ($16/month): Everything in Free, plus your own logo on the checkout page, a custom payment URL, no advertising, and email support. 25% discount if paid annually.

See full pricing →

When to Use QuickBooks Payments vs. a Payment Link Solution

Frequently Asked Questions

Can I use this with QuickBooks Desktop?

The Shuttle app is designed for QuickBooks Online. If you're on QuickBooks Desktop, you can still use Shuttle Links Checkout to send payment links to customers; the reconciliation back to QuickBooks Desktop would be manual.

Does this replace my payment gateway?

No. Shuttle connects to a supported gateway you already use. Your processing rates, merchant account, and settlement don't change. Shuttle adds the invoice payment link on top.

Is it PCI compliant?

Yes. Shuttle is a PCI DSS Level 1 service provider. Card data is handled securely and never touches your systems or QuickBooks.

Can customers save their card for next time?

Yes. Customers can opt in to save their details for faster payments on future invoices.

What about partial payments or deposits?

Supported. You can accept partial payments against an invoice. The remaining balance updates automatically in QuickBooks.

How fast do I get paid?

Settlement depends on your gateway. The key improvement is reducing DSO (days sales outstanding): customers can pay as soon as they receive the invoice, instead of arranging a manual payment.

Related Guides

• QuickBooks Payment Links: Add Pay Now to Any Invoice

• Authorize.net + QuickBooks: Complete Integration Guide

• What Is Embedded Payments?

• Payment Links for Stripe

• How to Choose a Payment Platform

• Stripe + QuickBooks Integration: accept invoice payments via Stripe

• Worldpay + QuickBooks Integration: pay invoices through Worldpay Access

• Braintree + QuickBooks Integration: accept payments via Braintree (PayPal + cards)

• PayPal + QuickBooks Integration: add PayPal to QuickBooks invoices