Syncing separate WooCommerce and Shopify stores to the same QuickBooks Company

Do you have both a WooCommerce site and a Shopify store and you'll like to connect both to the same QuickBooks Online company? We've got your back!

Written by the MyWorks Team

Updated at October 11th, 2023

Our WooCommerce and Shopify Sync for QuickBooks both support the ability to sync separate WooCommerce and Shopify stores to the same QuickBooks company if desired. As a reminder, you'll need one active plan for each WooCommerce or Shopify store you'd like to sync with QuickBooks.

Here's a couple tips and best practices to consider as you connect multiple stores to the same QuickBooks company. 

Separating Reporting in QuickBooks

Using Class/ Department for reporting

MyWorks supports setting a QuickBooks Class or Department to sync all orders to in MyWorks Sync > Settings > Order > QuickBooks Class or Department to be assigned to all orders.

For example, you can create one class for each ecommerce platform in QuickBooks, then set the appropriate class or department in MyWorks' settings for each corresponding site.

Then, orders synced to QuickBooks from each site will use the corresponding class, allowing easy reporting in QuickBooks.  

Using custom fields

MyWorks also supports custom field mapping - which can send a value or specific order field - into a specific field in a QuickBooks order ("memo"/ your own custom QuickBooks field). Some users opt for a value like "Store 1" to be custom mapped to one of these fields in QuickBooks - in which case QuickBooks reporting can be filtered utilizing this specific field.

Preventing order number conflicts

Now that orders from multiple sites are being synced into QuickBooks , there is a greater possibility for conflicting order numbers - for example: order number #545 existing on both systems, and attempting to sync to QuickBooks from both stores, which wouldn't be accepted in QuickBooks.

To guard against this possibility of conflicting order numbers, we have several best practices to choose from and adhere to:

  1. Use the “Next QuickBooks #” setting when syncing orders to QuickBooks. By default, we’ll sync orders from WooCommerce and Shopify into QuickBooks using the WooCommerce/Shopify order ID as the Invoice/Sales Receipt number in QuickBooks. But, when this setting is enabled, we'll sync orders into QuickBooks using the next QuickBooks invoice/sales receipt number – not the WooCommerce or Shopify order number.
  2. Using a custom order number extension in WooCommerce. By setting up custom order numbers in your WooCommerce store, you can add a store-specific prefix to each order number, which our sync will sync over to QuickBooks accurately.
  3. Syncing orders as Invoices vs. sales Receipts. If you have a WooCommerce store and a Shopify store connected to QuickBooks Online, a very simple solution is to set one store to sync orders over as Invoices + Payments, and the other store to sync orders over as Sales Receipts - and they will never conflict.