With a single warehouse, a count is mostly: count it, compare it to the sheet, done. But once you have two or three warehouses, things get complicated fast. If the same product sits as 10 units in your Tokyo warehouse and 5 in your Osaka one, looking only at the total of 15 to reconcile is meaningless. If Tokyo is short by 3 while Osaka is over by 3, the total still matches and the real problem stays hidden.
Shopify inventory is tracked per location from the start. So a count should also be done per location and reconciled per location. This time we follow the flow of matching each warehouse's physical count to the correct location column in your sheet, then tidying up the discrepancies.
Why count per location
In Shopify, inventory is recorded per location as states such as available, committed, and on hand. In other words, even for the same SKU, the quantity at warehouse A and warehouse B are entirely separate values. Count against the total only, and you lose sight of this per-location truth.
The biggest benefit of counting per location is that you can trace a discrepancy back to its source. When inventory does not match and it is happening at a specific warehouse, you can narrow the cause down to that warehouse's procedures or its inbound and outbound records. Look only at the total, and all you learn is that something is off somewhere, which makes the investigation far harder.
Carve out a count sheet per warehouse
If your master sheet holds every warehouse's inventory side by side in columns, handing that straight to the floor is not a good idea. It is far too easy for the Osaka person to accidentally overwrite a Tokyo column. Prepare a count sheet per warehouse that carves out only that warehouse's columns.
- 01From the master, pull out only SKU, product name, and the theoretical stock for the target warehouse
- 02Beside it, add an empty actual column and a difference column
- 03Put the warehouse name and date in the sheet name (e.g. count_osaka_2026-05-29)
- 04Share each warehouse's person only their own warehouse's sheet
- 05Protect everything except the actual column so the theoretical stock cannot be touched
Set the difference column to a formula of actual minus theoretical stock, so the gap shows the moment you type. Positive means over, negative means short, all at a glance.
Should you pause sync during the count
Here is the usual dilemma: is it fine to keep the auto-sync to Shopify running during the count? As a rule, pausing sync for the warehouse being counted is the safe choice. If that warehouse's quantity gets rewritten mid-count, you no longer know whether to trust the actual or the theoretical figure.
That said, you do not need to halt every warehouse at once. While Osaka is being counted, Tokyo can keep syncing as usual. Being able to split operations per location is a big strength of warehouse-by-warehouse counting. A tool that writes on-hand quantity per location, such as Sync Master, should pair well with this kind of per-warehouse pausing.
Reconcile per location
Once counting is done, it is time to reconcile. The iron rule here is: do not balance the books at the total level. On each warehouse's sheet, compare its theoretical stock against the actual, line by line. Lock in rows with zero difference; gather only the rows that show a difference into a separate list.
With multiple warehouses, an interesting phenomenon appears: the same SKU is minus 2 in Tokyo and plus 2 in Osaka. In most cases this is a sign of an unrecorded inter-warehouse transfer. A finding you could never have spotted from the total surfaces precisely because you went per location.
A matching total does not mean your inventory is correct. Inventory is only correct once it matches location by location.
Isolate causes per location
Once you have the difference list, isolate the causes per location. If discrepancies cluster at one warehouse, suspect a problem specific to that warehouse. If they are spread thinly across every warehouse, that may be a signal to rethink the product or SKU management rules themselves.
- Clustered at one warehouse: check that warehouse's inbound/outbound records and procedures
- Differences that cancel between warehouses: suspect a missed transfer record
- The same SKU short across several warehouses: suspect a shared shipping or return-processing gap
- Only high-value items off: review picking procedures and storage placement
Decide your response in order, starting with the ones whose cause you understand. Damage or loss: reduce as a write-off. A missed transfer: fix both warehouses' figures together. For discrepancies whose cause you cannot find, do not force them away; log them as unexplained discrepancies to feed trend analysis next time.
Steps to apply confirmed figures to the master
Once you have isolated the causes, return the confirmed actuals to the location columns of the master sheet. Here too, the key is not to mix warehouses. Osaka actuals into the Osaka column, Tokyo actuals into the Tokyo column, poured in one at a time, accurately.
Before applying, do confirm the column mapping with a connection test. Sync Master offers a connection test that lets you validate your column mapping before any real sync. By checking here which sheet column maps to which Shopify location, you prevent mix-ups like writing Osaka's numbers into Tokyo.
Once the master is updated, resume sync for the warehouses you had paused. If you use scheduled (automatic) sync, deciding a resume time after confirmation keeps your operation steady. Count per warehouse, reconcile per warehouse, apply per warehouse: keeping this one consistent flow makes a multi-warehouse count dramatically more trustworthy.
The more warehouses you add, the less you can get away with total-level fudging. That is exactly why you should build the habit of facing it per location from the start. On your next count, try beginning with a per-warehouse count sheet.