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Mintsoft and Shopify stock don't match: what to check

Updated 9 November 2026 · 6 min read · ShelfTrue team

If your 3PL runs on Mintsoft, Shopify's stock comes from Mintsoft's stock sync: on a timer, for one Shopify location, for the products it could match. When Shopify shows a number your warehouse can't ship, or sold out while the shelf is full, the cause is nearly always in that short list: the location on the connection, a SKU that doesn't match, inventory tracking off in Shopify, a paused store, or a sync that stopped. This guide goes through them in the order they're worth checking, then shows how to prove which products differ with one report from each side.

How Mintsoft updates Shopify

One direction. Stock goes from Mintsoft to Shopify. A number typed into Shopify never reaches Mintsoft and is overwritten at the next run.
On a timer. The connection has a stock update frequency in minutes and a “last run start” time. Between runs, Shopify keeps selling from its own count.
One Shopify location. The connection holds one Shopify Location ID: the location you ship from and that receives the stock. Other Shopify locations get nothing from Mintsoft.
Matched products only. Products are matched by SKU, which must be identical on both sides and is case sensitive. An option can limit the updates to active (not draft) Shopify products.

Mintsoft's help pages don't state which of its figures becomes Shopify's Available (on hand, or on hand minus allocated). Your warehouse can tell you which one their connection sends; the answer decides what you compare. If it's Mintsoft's available stock, compare it with Shopify Available. If it's on hand, expect Shopify to run higher than you can ship by every unit already allocated to an order being picked. Which Shopify number to trust, if the names are new to you.

Check these first

1. The location on the connection

In Mintsoft, Connect → Order Integrations → Shopify, click Get Locations and confirm the Location ID is the Shopify location your store sells from. A wrong or empty location means the stock goes to a location customers don't buy from, or nowhere. If you added a Shopify location recently, check that the connection still points at the one that fulfills online orders.

2. SKUs that don't match

Mintsoft needs the same SKU on both sides, spelled the same, same case, no leading or trailing spaces. A Shopify variant with no SKU, or a SKU that differs by a dash or a space, never updates and keeps the number it had. Bundles need their own match too. Fix the SKU in Shopify or in Mintsoft, then force one update by adjusting the Mintsoft stock level by one unit and back.

3. Inventory tracking off in Shopify

Shopify accepts a stock update only for products with Track quantity on. A product set to not track inventory sits at whatever number it shows and never changes. Open the product in Shopify, Inventory section, and turn tracking on at the location.

4. A paused store, or missing permissions

Stock updates work only with an active Shopify store; a store in Paused mode receives no updates. On the Mintsoft side the integration needs Read/Write permission, saved after any change.

5. The updates stopped

Two places tell you. In Mintsoft, the connection's last stock update run time. In Shopify, open a product, find the Inventory section, click View adjustment history and look for the Mintsoft app in the Created by column. A last entry from days ago while orders kept coming means the warehouse's numbers stopped arriving, and Shopify has been selling from stale counts since.

6. Back orders and "continue selling"

If a product is set to continue selling when out of stock, Shopify's Available can go negative when customers buy what isn't there. An update from the warehouse that sets Available to 0 clears that negative and, because On hand is Available + Committed + Unavailable, Shopify's On hand then rises to the committed count, which looks like stock appearing from nowhere. If you sell on back order, agree with your warehouse how a zero on the shelf should reach Shopify, and watch those products separately.

Find the products that differ

In Mintsoft, open Reports → Overview and run the Inventory Report (or Products In Locations) for your client and warehouse. Set Show Entries to 1000 before exporting, or you get only the first 20 rows. Export to CSV. Many warehouses can also schedule this report to arrive by email every day.
In Shopify, go to Products → Inventory, pick the location on the connection, and Export.
In a spreadsheet, match on SKU and subtract the Mintsoft figure your warehouse sends from Shopify Available. Rows that aren't zero are your list. Take both exports within the same hour so a sale in between doesn't add gaps of its own.

Note that Products In Locations leaves out products with zero stock, so a product sold out at the warehouse is missing from that report rather than listed as 0. Use the Inventory Report with its zero-on-hand option when you need the zeros.

Fix in this order

Connection first: location, permissions, store active, updates running. Until that's right, every number you correct drifts again at the next run.
Then SKUs and tracking for the products that never update.
Then counts, at the warehouse. Your warehouse adjusts Mintsoft; Mintsoft sends the number to Shopify. A hand edit in Shopify lasts until the next update.
Start with products where Shopify is higher and sells fast. Those oversell first.

Related guides

ShelfTrue does this check for you. Have your warehouse's daily Mintsoft stock report emailed to ShelfTrue, or upload it yourself. ShelfTrue reads the SKU and stock level from the report as it is, puts them next to Shopify Available for every linked product at that location, takes out orders still on their way, and lists the differences with the money at risk. We can look, but never change anything in Mintsoft.

Your first check is free.

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