Authorize.net is one of the most widely used payment gateways in the United States — and a significant number of Authorize.net merchants also run their books on QuickBooks Online. But connecting the two has always been harder than it should be.
QuickBooks doesn't natively support Authorize.net as a payment processor. If you want a "Pay Now" button on your invoices, Intuit wants you to use QuickBooks Payments — their own gateway. That means running two payment processors, two sets of fees, and two reconciliation workflows.
This guide shows how to connect Authorize.net directly to QuickBooks Online through Shuttle — so customers can pay invoices by card, and payments are automatically recorded in QuickBooks. No second gateway. No manual matching.
Why QuickBooks and Authorize.net Don't Connect Natively
QuickBooks Payments is Intuit's proprietary payment processor. It's the only gateway that gets native "Pay Now" button treatment on QuickBooks invoices.
This creates a problem for businesses that already use Authorize.net:
You're paying two sets of processing fees — Authorize.net for most transactions, QuickBooks Payments for invoice payments
Reconciliation is split — some payments come through Authorize.net, others through Intuit, and you're manually matching both
You lose your negotiated rates — Authorize.net merchants often have custom pricing built over years; QuickBooks Payments charges its standard rates
Your reporting is fragmented — transaction history lives in two places
The typical workaround is either accepting manual bank transfers (slow, no auto-reconciliation) or switching fully to QuickBooks Payments (losing your Authorize.net relationship).
Neither is good.
The Solution: Shuttle Connects Authorize.net to QuickBooks
Shuttle's QuickBooks Online Invoice Payments app bridges the gap. It connects your Authorize.net account to QuickBooks and adds a payment link to your invoices.
How it works:
Install the app and connect to QuickBooks Online
Enter your Authorize.net API credentials (API Login ID and Transaction Key)
Configure features (saved cards, partial payments, email notifications)
Paste the payment link into your QuickBooks invoice template
Customers click the link, pay by card on a secure checkout page
Payment is processed through Authorize.net
Payment is auto-recorded in QuickBooks against the correct invoice
Your Authorize.net account, rates, and settlement remain exactly as they are. Shuttle sits between QuickBooks and Authorize.net, handling the payment capture and reconciliation.
Setup Guide: Authorize.net + QuickBooks via Shuttle
Prerequisites
A QuickBooks Online account (Simple Start, Essentials, Plus, or Advanced)
An active Authorize.net merchant account
Your Authorize.net API Login ID and Transaction Key
Step 1: Install the Shuttle App
Go to shuttleglobal.com/quickbooks-online and click "Get App." You'll be redirected to authorise QuickBooks access — standard OAuth flow. Grant the required permissions.
Step 2: Connect Authorize.net
In the Shuttle dashboard, select Authorize.net as your payment gateway. Enter:
API Login ID — found in your Authorize.net account under Account → Settings → API Credentials & Keys
Transaction Key — generated from the same location
Shuttle validates the credentials immediately. If they're correct, you'll see a green confirmation.
Step 3: Configure Payment Settings
Enable the features that matter to your business:
Saved cards — let repeat customers save card details for faster future payments. Tokenised securely via Authorize.net's Customer Information Manager (CIM).
Partial payments — accept deposits or instalment payments against invoices. The outstanding balance updates in QuickBooks automatically.
Email notifications — get an email the moment a payment is received. Configurable to any email address.
Custom branding (Basic plan, $16/month) — add your logo to the checkout page and use a custom payment URL.
Step 4: Add Payment Link to Invoices
Copy your unique payment link from the Shuttle dashboard. In QuickBooks Online:
Go to Settings → Custom Form Styles
Edit your invoice template
In the message/notes section, paste: "Pay online: [your payment link]"
Save
Every invoice you send now includes a clickable payment link. Customers on desktop or mobile can tap and pay.
Alternatively, paste the link into individual invoices when you want to offer online payment selectively.
What Happens When a Customer Pays
Customer opens your QuickBooks invoice via email
They click the payment link
A secure checkout page opens (Shuttle-hosted, PCI DSS Level 1)
They enter card details or use a saved card
Transaction is processed through your Authorize.net account
Funds settle to your Authorize.net merchant account (your usual rates and timeline)
The payment is automatically recorded in QuickBooks — invoice marked as "Paid"
The entire flow from customer click to QuickBooks reconciliation is automatic. No manual intervention.
Authorize.net Features That Work Through Shuttle
Authorize.net Feature | Supported via Shuttle |
|---|---|
Card processing (Visa, MC, Amex, Discover) | Yes |
Customer Information Manager (saved cards) | Yes |
Address Verification Service (AVS) | Yes |
Card code verification (CVV) | Yes |
Fraud detection suite | Yes — your Authorize.net fraud settings apply |
Recurring billing via Authorize.net ARB | Not directly — use Shuttle's partial payments for instalments |
eCheck / ACH | Depends on configuration |
Level 2/3 data | Yes — passed through where applicable |
Your existing Authorize.net fraud filters, velocity checks, and security settings remain active. Shuttle processes the transaction through your account — it's your Authorize.net configuration that governs the rules.
Pricing
Shuttle Free plan:
Auto-record payments in QuickBooks
Saved cards
Partial payments
Email notifications
PCI DSS Level 1 compliant
No Shuttle transaction fee (your Authorize.net rates apply)
Shuttle Basic plan ($16/month):
Everything in Free
Your logo on the checkout page
Custom payment URL
No advertising on checkout
Email support
25% discount if paid annually
Authorize.net fees remain yours. Shuttle doesn't add to or change your Authorize.net processing rates. Your standard per-transaction fees apply as normal.
Common Questions
Will this affect my Authorize.net account?
No. Shuttle processes transactions through your existing Authorize.net account using the standard payment gateway API. Your account, rates, settlement, and reporting remain unchanged. Transactions processed via Shuttle appear in your Authorize.net reporting alongside all other transactions.
Can I use both QuickBooks Payments and Authorize.net via Shuttle?
Technically yes — QuickBooks Payments for native "Pay Now" button and Authorize.net via Shuttle for payment links. But this creates the dual-stack problem. Most merchants find it cleaner to use Shuttle exclusively, since it provides auto-reconciliation through your preferred gateway.
Does this work with Authorize.net sandbox/test accounts?
Yes. You can connect a sandbox Authorize.net account for testing before going live. Process test transactions, verify auto-reconciliation in QuickBooks, then switch to your production credentials.
What if I also use Authorize.net for my website or POS?
No conflict. The Shuttle integration uses your Authorize.net account for invoice payment links only. Your existing website checkout, POS, or any other Authorize.net integrations continue to work independently.
Is Authorize.net CIM (saved cards) PCI compliant through Shuttle?
Yes. Shuttle is a PCI DSS Level 1 service provider. Card data is tokenised during the checkout flow. Saved card tokens are stored via Authorize.net's Customer Information Manager — the most secure tokenisation method available through Authorize.net.
I'm in the UK/EU — can I use this?
Authorize.net primarily serves the US market. If you process payments internationally, check whether your Authorize.net account supports international transactions. Alternatively, if you use a gateway like Worldpay or Stripe for international transactions, Shuttle connects to those as well — see our QuickBooks invoice payments guide for the full list.