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Fix Shopify inventory mismatch

Find why Shopify stock does not match your warehouse CSV — missing SKUs, quantity diffs, untracked inventory — and how to compare files then fix quantities before re-import.

A Shopify inventory mismatch means the quantity (or presence) of SKUs in Shopify does not match your supplier, warehouse, or POS spreadsheet. This guide covers the usual causes and a CSV-first way to detect and fix them.

Common causes

SymptomLikely cause
Qty differs for the same SKUStale Shopify export, unsynced location stock, or bad spreadsheet edit
SKU in warehouse file but not ShopifyProduct never created, wrong SKU, or draft/unpublished product
SKU in Shopify but not warehouse fileDiscontinued item still active, or incomplete count file
Qty looks right but storefront is wrongInventory not tracked, wrong location, or policy/oversell settings

Inventory policy does not change on-hand quantity, but continue can make the storefront sell when qty is already 0 — which feels like a mismatch. See variant inventory policy.

Compare two CSVs (free tool)

Use Compare inventory — no account required:

  1. Export products from Shopify Admin (include Variant SKU + inventory qty)
  2. Prepare your warehouse/supplier file with SKU + quantity columns
  3. Upload both files on the compare page
  4. Review quantity mismatches, missing in supplier, and missing in Shopify
  5. Download the mismatch report CSV

Fix quantities in Import Ready

  1. Upload the file that should become the source of truth
  2. Match columns for SKU and stock quantity (and policy if present)
  3. Bulk edit wrong quantities using search by SKU
  4. Validate and export Shopify product CSV
  5. Re-import into Shopify Admin (or update inventory with your usual process)

Checklist

  • SKUs match exactly (trim spaces, consistent case)
  • You are comparing the same location / warehouse scope
  • Inventory tracker is shopify for variants that should be tracked
  • Policy is deny unless you intentionally oversell
  • You validated the full file before Admin upload

Related guides

Previous

Shopify inventory CSV template

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Bulk fix spreadsheet errors