Our Shopify Sync supports syncing multiple Shopify stores to either a single QuickBooks Online company; or each to their own. As a reminder, you'll need to install our app in each Shopify store you'd like to sync with QuickBooks.

There are a couple of tips that can be helpful as you sync multiple Shopify stores to a single QuickBooks Online company.

Order number conflicts

Since orders from multiple stores are being synced into QuickBooks Online, there is a greater possibility for conflicting order numbers - for example: order number #1093 existing on both stores, and attempting to sync to QuickBooks Online from both. In this case, since QuickBooks Online doesn't allow multiple orders with the same number; one of these orders would not sync to QuickBooks.

To avoid this possibility of conflict, there's several approaches we recommend considering:

1. Setting a custom order number prefix or suffix in your Shopify settings for each store - and enabling our setting in Settings > Order to use the Shopify Custom Order number.
2. Setting a prefix in our sync in MyWorks Sync > Settings > Order - differently for each store - which we'll then use to ensure order numbers in QuickBooks are unique between multiple stores.  
3. Using our “Next QuickBooks #” setting.  This is the best option if you're also entering orders manually in QuickBooks as well! This results in the Shopify order being created in QuickBooks using the next available number in QuickBooks, instead of the Shopify order number. The result would be your QuickBooks order numbers being perfectly sequential, regardless of which Shopify store they were synced from, or if they were also entered manually in QuickBooks.