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How to move Shopify inventory to a third-party warehouse, step by step

Updated 23 November 2026 · 6 min read · ShelfTrue team

Shopify counts stock per location, so moving to a third-party warehouse means three things in order: give the warehouse its own location, move the quantities there with a transfer, then send online orders to it. Keep the old location until it is empty and has no open orders, and only then switch it off. Done in that order, you always know where each unit is counted.

Before you start: write down what you have now

Don't change any number yet. First keep a record of the stock you are about to move.

In Shopify admin, go to Products, then Inventory, and click Export.
In Export from, choose the location the stock is leaving. Under Inventory states shown, choose All states. Choose All variants, then click Export inventory.
The file has one row per variant and location, with Committed, Available and On hand. Keep it. It is your count before the move and the list you will check the warehouse's receiving count against.

Ask the warehouse what they need on their receiving paperwork. Make sure every variant you send has an SKU in Shopify and that the warehouse uses the same SKU.

Step 1: Give the warehouse a location

Ask the warehouse how they connect to Shopify before you create anything. One warehouse with two locations means two counts to keep apart.

If the warehouse connects through its own app, Shopify treats it as a location. You will see it in Settings, then Locations, under App and custom fulfillment locations. App locations don't count toward your location limit.
If you will keep the counts in Shopify yourself, add a location: go to Settings, then Locations, and click Add location. Enter a name your team will recognize and the warehouse address, then save. Shopify adds the new location to the bottom of your order routing list.

A new location has the setting Inventory at this location is available to fulfill online orders turned on by default.

Step 2: Make the products active at the new location

A product only sells and ships from locations where it is active. On the Inventory page, a dash in the Available column means the product is inactive at that location. Moving stock to a location with a transfer adds quantity there, but it does not make the product active.

Go to Products and open the product.
In the Inventory section, click Edit locations.
Select the warehouse location, click Done, then click Save.

Products you create from now on are assigned to all your locations with a starting quantity of 0.

Step 3: Move the stock with a transfer

If the warehouse location is run by the warehouse's app, ask the warehouse first how their receiving count reaches that location. Their system's own help center is the place to check that rule. For a location you added yourself:

Go to Products, then Transfers, and click Create transfer.
In Select origin, choose the place the stock is leaving. In Select destination, choose the warehouse location.
Click Search products, select the products, and click Add. In the Move column, enter the quantity for each one, using your export.
Save the transfer. It is a draft, and nothing is committed yet.

Then follow the goods:

When	What you do in Shopify	What the numbers do
The stock is packed to leave	Mark the transfer as ready to ship	The units are Committed at the origin location
It is on the way	Move the transfer to in transit	The units show as incoming at the warehouse location
The warehouse confirms what it received	Receive the transfer	Once it is marked as transferred, the units are available at the warehouse location
The trip is called off	Cancel the transfer	The committed units are made Available at the origin again

While a transfer is ready to ship or in transit, those units can't be sold from either location: they are committed at the old one and only incoming at the new one. Move in batches, or pick a quiet day.

Receive what the warehouse counted, not what you sent. If the warehouse counted fewer, ask about that shipment before you correct anything in Shopify. A gap found on receiving day is a question about one shipment. The same gap found a month later is much harder to explain.

Step 4: Send online orders to the warehouse

Order routing only applies when a store has two or more locations that fulfill orders. Now you have two, so decide which one ships first.

Go to Settings, then Shipping and delivery. In the Shipping section, click Order routing, then the arrow icon to open it.
Click Add rule, then click Use ranked locations.
Drag the new rule to the top of the list.
Click the pencil icon on the rule. Drag the warehouse location into the topmost location group, and leave the locations that should not come first in the bottom group.
Click Done, then click Save.

Step 5: Switch off the old location

Wait until the old location's On hand is zero, or holds only stock that is meant to stay there, and its orders are fulfilled.

Orders placed during the move may still sit at the old location. To move one to a location you manage, go to Orders, open the order, click the ... button and choose Change location.
If the old location is your default location, change the default first: Shopify won't deactivate the default location. In Settings, then Locations, find Default location and click Change.
To stop selling and fulfilling from the old location, go to Settings, then Locations, click the location, and click Deactivate location. If it still has inventory, orders or transfers, Shopify asks you to choose another location to receive them. Then confirm.
You always need at least 1 active location. A deactivated location can't fulfill orders and can't be your default location.

Step 6: Check the counts after the move

Export again: Products, then Inventory, then Export. In Export from, choose the warehouse location, and choose All states.
Ask the warehouse for their stock report from the same day. Compare Shopify's On hand for each SKU with the units they have on the shelf. Committed shows orders that are taken but not shipped yet, so look at those before you call a gap wrong. Available and On hand are two different numbers.
To correct one product, go to Products, then Inventory, pick the warehouse location in the location picker, and click the quantity in the Available or On hand column. Enter the number in Set to, click Add reason to record why, click the check icon, then click Save.

Don't fix the counts by importing the file you exported before the move. When a file has both On hand (current) and On hand (new), Shopify compares it with today's levels and skips the rows that changed since the export, then emails you the list. Clearing On hand (current) removes that check, so an old file can overwrite stock that has moved since.

After the move, a weekly reconciliation routine keeps the two counts together.

Related guides

ShelfTrue does the comparing after the move. Upload your warehouse's stock file, or have your warehouse email it to ShelfTrue, and it compares it with Shopify for every linked product at that location, takes out the differences that are only paid orders on their way, and lists what is left with the money at risk. We can look, but never change anything at the warehouse.

Your first check is free.

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