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 without switching away from your existing payment gateway.
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 plug into 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
ACH and card payments supported
Limitations:
US only
Intuit sets the processing rates (2.99% card, 1% ACH with $10 max)
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 your existing payment gateway 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:
Connect your gateway — Authorize.net, Braintree, PayPal, Stripe, Worldpay, and more
Get a payment link — a unique URL tied to your QuickBooks account
Paste into invoices — add the link to your invoice template or individual invoices
Customer pays — they click, enter card details (or use Apple Pay / Google Pay), and pay
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 settlement, 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 your international-capable gateway to QuickBooks.
More payment methods. Depending on your gateway, customers can pay by card, PayPal, Apple Pay, Google Pay, and local payment methods — more options than QuickBooks Payments offers natively.
How to Set It Up (5 Minutes)
Setting up online invoice payments in QuickBooks via Shuttle takes about 5 minutes:
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** — the most popular gateway among QuickBooks users (full integration guide)
Stripe — if you already process cards through Stripe
Braintree — PayPal's gateway for card processing
PayPal — direct PayPal payments
Worldpay — 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 the moment 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:
They click the link
A branded checkout page opens (your logo on the Basic plan)
They enter card details or choose Apple Pay / Google Pay
Payment is processed through your gateway
They see a confirmation
The payment is auto-recorded in QuickBooks against the correct invoice
No account creation. No app download. No friction. Just click and pay.
Auto-Reconciliation: The Real Time Saver
The biggest operational win isn't the faster payment — it's the automatic reconciliation.
Every payment processed through the link is recorded back into QuickBooks against the correct invoice. The invoice status updates to "Paid" (or "Partial" for deposits). Your books stay accurate without anyone manually matching bank statements to invoices.
For businesses sending 50+ invoices per month, this eliminates hours of manual reconciliation 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.
When to Use QuickBooks Payments vs. a Payment Link Solution
Scenario | QuickBooks Payments | Payment Link (Shuttle) |
|---|---|---|
US-only, no existing gateway | Good fit | Works, but unnecessary |
Existing gateway relationship | Forces you to switch or run two stacks | Keep your gateway |
International invoicing | Not supported | Works with any international gateway |
Multiple payment methods | Cards + ACH | Cards, PayPal, Apple Pay, Google Pay, local methods |
Custom branding | Limited | Full branding on Basic plan |
Multi-PSP environment | Single provider only | Connects to 40+ gateways |
Auto-reconciliation | Built in | Built in |
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 Payment Links 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 your existing gateway. 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. The saved card feature works with all supported gateways. 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 — typically 1-2 business days for card payments. The key improvement is reducing DSO (days sales outstanding): instead of waiting 30-45 days for a manual payment, customers pay within days of receiving the invoice.