MyWorks supports syncing inventory levels from QuickBooks Desktop to Shopify, any time inventory is changed in QuickBooks. And, when orders are placed on Shopify, those will correctly reduce inventory in QuickBooks as we sync the order into QuickBooks.
There's a few factors to keep in mind before enabling inventory sync - in MyWorks Sync > Settings > Automatic Sync. We'll sync inventory for any products that meet the below conditions:
- The product needs to be an inventory product in both Shopify and QuickBooks Desktop.
- The products must be mapped together in Map > Products/Variations in our sync.
Once the above conditions are met and inventory sync is enabled in MyWorks Sync > Settings > Automatic Sync, we'll start syncing inventory levels: from QuickBooks to update Shopify to match. If you're not managing inventory in a Shopify or QuickBooks product, we won't sync inventory for that product.
MyWorks also supports customizing how inventory is synced in the below ways:
- Supporting inventory sites in QuickBooks Desktop, and Locations in Shopify
- Syncing the Available or Quantity on Hand inventory levels from QuickBooks
Handling multiple Shopify Locations
When you have more than one location in Shopify, MyWorks has strong support to sync inventory levels from QuickBooks to Shopify.
- If you also use Inventory Sites in QuickBooks Desktop, you can map these to individual Shopify Locations so MyWorks can sync inventory between them.
If you don't have separate Inventory Sites in QuickBooks, MyWorks syncs inventory by changing inventory for one Shopify location to result in the total inventory in the Shopify product (across all warehouses) matching the QuickBooks inventory level. You can choose which Shopify Location we sync inventory changes to, by selecting this in MyWorks Sync > Settings > Product:

Once set, inventory would sync like the below example:
Starting: QuickBooks has 12 in stock, and the Shopify product also has 12 total:
Location 1 - 3 in stock
Location 2 - 4 in stock
Location 3 - 5 in stock
Then: QuickBooks changes to 14. We'd update the Shopify location set in our settings above - which for example, is Location 2. This would result in this Shopify product having:
Location 1 - 3 in stock
Location 2 - 6 in stock
Location 3 - 5 in stock
Syncing the Available or Quantity on Hand levels
MyWorks supports syncing either the Available inventory level or the Quantity on Hand inventory level from QuickBooks items into Shopify. This setting can be easily adjusted in MyWorks Sync > Settings > Product.
The “Available” Inventory level in QuickBooks is made up of the Quantity on Hand level, minus any inventory used in Sales Orders.

Syncing “Max Available” inventory for Inventory Assembly Items
MyWorks also supports syncing the “Max Available to Built” quantity for Inventory Assembly items from QuickBooks to Shopify so that Shopify reflects the most that can be sold for that particular item in QuickBooks.
%20%C2%B7%20MyWorks%20QBD%20Sync%20-%20Staging%20%C2%B7%20Shopify%202025-09-02%20at%208.14.52%20AM.png)
Exclude Shopify Warehouses when syncing inventory
By default, MyWorks will update the Shopify product inventory so that its total matches the total inventory for that item in QuickBooks (unless Shopify Locations/Warehouses are mapped to individual QuickBooks inventory sites).
This means that if a Shopify product has 3 locations, MyWorks will update the inventory of the selected location, to ensure the total of that product across all locations matches QuickBooks. For example, if there's 100 in stock in each of the three locations in Shopify, and the QuickBooks product has 350 in stock, MyWorks will update the selected Shopify location to 150.
However, there may be cases where MyWorks shouldn't factor in the inventory in other Shopify locations when syncing inventory; and this can be set in MyWorks Sync > Settings > Product as shown below: excluding specific Shopify warehouses when syncing inventory. Any warehouses/locations set here would not be included in the inventory calculation we make as we update the Shopify product inventory from QuickBooks.
%20%C2%B7%20MyWorks%20QBD%20Sync%20-%20Staging%20%C2%B7%20Shopify%202025-09-02%20at%208.17.03%20AM.png)