If you sell on your own Shopify store and on Amazon, the two systems will disagree about stock at some point. Usually nothing is lost. The two numbers just mean different things, or a product is mapped wrong, or one system hasn't caught up with an order yet.
A connector app can move numbers between systems. It can't decide what those numbers mean or who fixes a mismatch. This page covers the setup that makes sync work, and how to find the cause when it doesn't.
Decide how stock is shared
Start with the physical setup, because it decides what can go wrong. Most brands use one of these:
- Separate pools. Shopify orders ship from your warehouse, and Amazon orders ship from FBA. The numbers don't need to match, but you still need to know when to move stock from one to the other.
- One shared pool you ship yourself. Both channels sell from the same shelf. Every order on one channel has to reduce the quantity available on the other, quickly.
- FBA stock for both channels. Amazon's Multi-Channel Fulfillment can ship your Shopify orders from FBA inventory. Amazon's numbers become the main record.
Write down which setup each product uses, which location holds the stock and who can change an allocation.
Map every product properly
Most sync problems start with a bad map. For each item, match:
- The Shopify product variant.
- The Amazon seller SKU and marketplace (Amazon.ca and Amazon.com are separate).
- The physical pack size.
- Bundle contents.
Check pack size and bundle contents, not just the product name. If a two-pack on Amazon is mapped to a single bottle in Shopify, every Amazon order takes one bottle out of the count instead of two. The totals drift slowly, and nobody notices until a customer order can't be filled.
Look for duplicate SKUs and old variants that are still mapped. They cause double deductions.
Define what each number means
Shopify and Amazon split stock into different states.
Shopify tracks quantities such as on hand, available, committed (held for unfulfilled orders), unavailable and incoming.
Amazon's FBA reports separate fulfillable units from inbound, reserved and unfulfillable units. Reserved stock includes units held for customer orders and units moving between fulfilment centres.
A Shopify "available" figure isn't the same as Amazon's fulfillable figure, and neither equals the total on the shelf. Label each quantity in your records by what it actually means: physically held, available to sell, reserved or awaiting receipt. Compare like with like.
Set reservation rules for shared stock
If both channels sell from one pool, each unit committed to one order must be held so it isn't sold again on the other channel. Decide and record:
- Which events reserve a unit: order placed, payment captured or order released to the warehouse.
- When a cancellation releases the unit.
- How returns come back into stock, and who inspects them first.
- How damaged, expired or quarantined units are kept out of available quantities.
- Whether to hold a small buffer back from one channel, so a short delay in sync doesn't cause an oversell.
When the numbers disagree
Don't change every stock figure at once. A broad reset hides the cause and makes the next mismatch harder to trace. Work through one product at a time:
- Record the basics. Marketplace, seller SKU, Shopify variant and pack size.
- Save both exports with their times. Note each report's export time and what its quantity means.
- Find a shared cut-off. Compare figures from the same point in time where you can.
- List what happened in between. Orders, cancellations, returns, transfers and receipts between the two export times.
- Check reservations. Is one number including units that are reserved or can't ship yet?
- Check the map. Look for duplicate identifiers or a bundle mapped as a single item.
Amazon notes that its inventory reports are snapshots. Account for the movements between reports before deciding that a connector or a location balance is wrong.
Correct the record on purpose
Once you know the cause, write it down and identify the record that supports the correction. Make only that correction, then check both systems again. Keep the movement record and the new balance together.
If the same difference comes back, the cause is upstream. Review the mapping, the reservation rule or the handoff that created it. Fixing the number each week without fixing the cause just repeats the work.
Trace one order end to end
A good test after any setup change: pick one real order or stock transfer and follow it through every step. Check the source record, the reservation, the shipment and the final quantity on both channels. Duplicate deductions, missed releases and unmatched identifiers show up quickly this way.
If you use a connector app
Write down:
- What access it has to each account.
- Which products and locations it syncs, and how often.
- What it does when an update fails, and who gets told.
- Who on your team owns its settings.
Test a known movement after any change to the app, the catalogue or the warehouse setup. A working connection still needs regular checks and a person who handles the exceptions.
Why it matters on Amazon
Overselling on your own store means an apology email. On Amazon, cancelled orders and late shipments count against account health, and a stockout can cost the listing its momentum. Our page on stockouts on Amazon covers what to check if one happens. If ads keep running while stock is low, see stock-aware Amazon advertising.
How we handle this
Checking stock across channels is part of our weekly inventory and replenishment work. We keep one record of what's sellable, what's on the way and what doesn't match, with a person responsible for each open item.
Want a quick look at your Amazon listings first? Get a free Amazon check. No account access needed.