Understand Shopify On Hand vs QuickBooks Physical Stock in Webgility Desktop

Customers often open a ticket because Shopify shows a SKU with one or more units on hand while QuickBooks shows zero for the same item. This article explains why the two numbers can disagree even when Webgility Desktop is syncing correctly, and which Webgility setting decides what gets pushed.

This applies if you see a SKU in Shopify with a non-zero On hand value while QuickBooks shows zero physical stock for the same item, and you sell the SKU on multiple channels or take pre-orders that remain unfulfilled.

Shopify's On hand figure is the total quantity your store is holding, including units that are already committed to orders not yet fulfilled. QuickBooks on-hand, by contrast, is the physical count after every posted transaction. So a SKU with one unit sold but not yet shipped reads as 1 on hand and 1 committed in Shopify while reading as 0 in QuickBooks, and both numbers are correct.

Important Note: "Webgility Desktop pushes the quantity you choose in Product Sync Settings. If you want the channel to reflect only what is physically available for sale, point Webgility at available quantity, not on-hand quantity."

Steps to Reconcile the View in Webgility Desktop

Step 1: Open Webgility Desktop and go to Products > Settings > Sync Settings to open the Product Sync Settings dialog (for the full field reference, see How to Sync Products with Webgility Desktop).

Step 2: Confirm Select your master catalog names the side you treat as the authoritative stock source, which for most QuickBooks users is QuickBooks.

Step 3: Set Specify which quantity to use for sync to Available quantity if you want the pushed number to exclude units already committed to open orders, or leave it on On hand quantity if you want the full physical count including committed.

Step 4: Click Save & Close and wait for the next Scheduler run, then open the SKU in your Shopify admin and confirm the pushed number matches the choice you just made.

Step 5: If Shopify On hand is still higher than expected, open each unfulfilled order in Shopify and check the committed count against the gap (for how forecasting treats committed stock, see How to Optimize Cashflow with Inventory Forecasting).

Choose a single definition of the number you want to see on each channel, set it once in Product Sync Settings, and compare like for like — on-hand with on-hand, available with available — when auditing discrepancies. The two figures are different by design, not by mistake.

If the Shopify On hand value does not match your chosen setting after the next sync, email support@webgility.com with the SKU, the Shopify On hand and committed values, and the QuickBooks on-hand value at the same moment.