Guide: Setup QuickBooks Online Integration

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 from Allmoxy

• Important Settings to Review

• Set up your integration

• Troubleshooting & Common Issues

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

Payment made before invoice creation:

• Payments will appear in QuickBooks under the customer's account in "Unapplied 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.

Here are some steps we recommend following prior to connecting your Quickbooks Online to Allmoxy! 

Step 1: Confirm You Have the Right Permission

The Integrations → Accounting tab only appears for users with the Manage Accounting permission. If you don't see it, ask your instance primary contact (or your Customer Success Manager) to enable that permission on your account, then refresh the page.

Step 2: Review Allmoxy Export Classes & QBO Products/Services

Allmoxy's Export Classes map to QBO Products/Service which maps to desired Revenue (Income) account. To ensure your revenue is tracked correctly, make sure you have reviewed your Allmoxy products' export classes, and that those corresponding QBO Products/Services are mapped to your desired Income Account. 

Step 3: 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

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 4: 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

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.

Step 5: Disable Any Other Accounting/Payment Integrations

If you've previously used another tool to push invoices or payments into QuickBooks; for example, a Stripe-based tracker, Zapier automation, or a similar connector — turn it off before connecting Allmoxy. Running two integrations at once causes duplicate invoices in QuickBooks (see Troubleshooting).

 

Set Up Your Integration: 

Set Up Your Default Export Class

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.

Export Classes map your Allmoxy products to a Product/Service in QuickBooks Online, which in turn maps to a Revenue/Income account. Every invoice line item in QuickBooks must reference a Product/Service. A product with no Export Class won't transmit. QuickBooks will automatically create the Product/Service based on the Default Export Class determined in Allmoxy if it doesn't already exist. 

Mapping at a glance:

• Export Class → QuickBooks Product/Service
• Allmoxy product name → QuickBooks line description

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.

Confirm or Assign Export Classes in bulk:

• In Allmoxy, go to Utilities → Product Updater
• In the left sidebar, scroll below the categories to the editable-field section and select Export Class
• Click Get Products to pull your full catalog, then fill in any blank Export Class fields so each product points to the correct QuickBooks Product/Service
• Tip: you can focus on products where Available for Sale = Yes, or simply update everything in one pass

Doing this before connecting prevents products from landing in the wrong Product/Service, which is harder to clean up in QuickBooks afterward.

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!