Guide: Setup QuickBooks Online Integration
This guide walks you through the setup process and the critical settings you need to adjust before connecting.
Allmoxy's QuickBooks Online integration automatically syncs your financial data between systems, eliminating duplicate data entry and ensuring your accounting records stay up-to-date.
What Gets Synced
Once connected, Allmoxy automatically syncs the following financial data to QuickBooks Online every 2 hours:
📄 Orders and Invoices
- Orders sync to QuickBooks as Estimates
- When the order reaches your "Status to Charge Customer" setting in Allmoxy, the estimate converts to an Invoice
- Status to Charge Customer is a global financial setting: commonly set to "Shipped" status, but can also be overridden at the customer level (for example, a specific customer might be set to charge at "Completed" status instead)
💳 Payment Processing
Turn off the auto-apply payments setting in your Quickbooks to ensure that payments apply to the corresponding invoice instead of the oldest open balance.
Payment made before invoice creation:
- Payments will appear in QuickBooks under the customer's account in "Undeposited Funds"
- Once the estimate converts to an invoice, the payment automatically applies to that invoice
Payments made after invoice creation:
- Payments post directly to the corresponding invoice
Other Financial Data
These items sync upon generation:
- Finance charge invoices
- Credit memo invoices
- Processing fees invoices
- Customer information
You'll see a "Last Run" timestamp on the integration page showing when the last sync completed.
⚠️ IMPORTANT: Some settings in QuickBooks Online MUST be adjusted before connecting Allmoxy. Skipping these steps will cause significant issues with your invoices and payments.
Step 1: Turn OFF QuickBooks Sales Tax
Allmoxy sends sales tax information as a line item on each invoice. If QuickBooks Sales Tax is enabled, you'll end up with duplicate taxes on every invoice.
How to turn off Sales Tax: (Disregard if you've never set up Quickbooks Sales Tax)
- Log into QuickBooks Online

- Hover over All Apps on the left sidebar
- Select Sales Tax > Overview
- Find Sales Tax Settings
- Select Turn off sales tax
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Why this matters: Using both Allmoxy's tax calculations and QuickBooks' Sales Tax feature will result in doubled tax amounts on your invoices, creating major reconciliation headaches.
Step 2: Turn OFF Automatically Apply Bill Payments
This QuickBooks setting automatically applies payments to the oldest open invoice in your account. When enabled, it ignores which specific invoice you're paying in Allmoxy.
How to turn off this setting:
- Log into QuickBooks Online
- Click the gear icon in the upper right
- Select Account and Settings
- Navigate to Advanced → Automation
- Toggle OFF the Automatically apply bill payments setting
- Click Save
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Why this matters: Allmoxy's integration applies payments to the exact invoices you specify within Allmoxy. The automatic payment feature will override this, causing payments to be applied incorrectly.
To Setup the Integration: Set Up Your Default Export Class
Before connecting, you'll need to define a Default Export Class in Allmoxy. This is mapped to the Product/Service field in QuickBooks Online.
What is a Default Export Class? A Default Export Class is used when a product in Allmoxy doesn't have a specific Export Class assigned. This ensures all financial data transmits properly to QuickBooks.
Common examples include:
- Cost of Goods Sold
- Cabinets
- Wood Products
- Materials
Choose whatever makes sense for your QuickBooks chart of accounts. You can always update individual products with more specific export classes later.
Connecting Allmoxy to QuickBooks Online:
Once you've adjusted the required settings in QuickBooks, you're ready to connect:
-
Navigate to the Integration Page
- In Allmoxy, go to Integrations ➡️ Accounting in the main menu
- Select QuickBooks Online
-
Enter Your Default Export Class
- Type your default export class in the provided field
- This activates the "Connect to QuickBooks" button
-
Connect to QuickBooks
- Click Connect to QuickBooks
- You'll be redirected to QuickBooks to sign in
- If you have multiple QuickBooks companies, select the one you want to sync your Allmoxy instance to
- Review the permissions and data access information
- Click Connect
-
Connection Confirmed
- You'll be redirected back to Allmoxy
- Your connection status will show as "Connected"
- The integration will begin syncing on the next batch run (every 2 hours)
Using a Sandbox Environment (Optional)
If you want to test the integration before going live with your production data, you can connect to a QuickBooks sandbox environment first.
To switch from Sandbox to Production:
- Click Disconnect on the QuickBooks Online integration page
- Click Connect to QuickBooks again
- Sign in with your production QuickBooks account credentials
- Complete the connection process
This allows you to test the integration thoroughly without affecting your live accounting data.
Managing Your Connection
You can view and manage your QuickBooks connection at any time:
- Environment: Shows which QuickBooks company you're connected to (Production or Sandbox)
- Status: Displays whether the integration is Active or Inactive
- Last Run: Shows when the last sync completed
To disconnect or switch environments, simply click Disconnect and follow the connection process again with your desired QuickBooks account.
Need Help?
If you encounter any issues during setup or have questions about the integration, reach out to your Customer Success representative. We're here to ensure your QuickBooks integration runs smoothly!