A · Export inventory from Shopify
In Shopify Admin, go to Products > Inventory > Export and choose All states. Use a fresh file for the locations in your count.
Public BetaReview every prepared inventory change before importing it.
A SIX-STEP, HUMAN-REVIEWED WORKFLOW
From physical count to reviewed file
Use CountAlign only when you already have a count file created outside Shopify. If you still need to count products, start with Shopify’s built-in inventory count.
B · Prepare the physical count CSV
Use one row per counted variant and location. Include a stable SKU or Handle with option values, a whole-number Counted value, and the exact Location for multi-location stores.
C · Upload the two files
Select the Inventory CSV and count CSV. Add the current Shopify Product CSV only if your count sheet uses Barcode values.
D · Review exceptions
Check exact matches, changed quantities, unchanged rows, ambiguous identifiers, unmatched rows, invalid values and location warnings. The tool never guesses an ambiguous identity.
E · Download the prepared file and report
Download the prepared All states Inventory CSV and the exception report. The tool changes only On hand (new) for eligible quantity differences and keeps the exported baseline.
F · Inspect manually before import
Inspect every proposed quantity and location in the downloaded file. Import it from Shopify Admin only if it is right, then review Shopify’s import summary.
Choose the right counting workflow
Counting directly in Shopify?
Use Shopify's built-in stock counts when you want to plan a count for a location and review differences in Admin. Staff can count in Shopify POS with POS Pro (Shopify POS v11.16 or later); changes are applied after Admin review and approval. Use CountAlign when a physical-count CSV created elsewhere is already prepared.
Shopify inventory stock-count guide ↗Already have a physical-count CSV?
Use CountAlign to match those counted rows to Shopify Inventory CSV before import. CountAlign prepares only rows that meet its exact variant and location rules.