Selling the same products on your Shopify store and on Amazon is one of the most common multichannel setups, and one of the easiest to get wrong. Each platform keeps its own stock count. Unless something keeps them together, a sale on one does not reduce the other, and sooner or later you sell a unit twice.
This guide walks through the options, the setup decisions that matter and a test plan, so the sync works on day one and stays working.
In short: pick one system as the source of truth, map every Shopify variant to its Amazon SKU, treat FBA stock separately from your own warehouse stock, sync Shopify's available quantity (not on hand), and test with a real order on each side before you trust it.
Decide What You Are Syncing
"Syncing Shopify and Amazon" is really four separate flows. Decide which you need:
| Flow | Direction | Why It Matters |
|---|---|---|
| Stock levels | From your source of truth to both channels | Prevents overselling |
| Orders | From both channels into one place | Lets one team ship everything and reserves stock |
| Listings and prices | From your catalog to the channels | Saves double entry, keeps details consistent |
| Tracking | From your shipping tool back to the channel that sold | Orders show as shipped, metrics stay healthy |
Stock and orders are the core. Listings and tracking are where most of the time savings are.
Pick One Source of Truth
Exactly one system should own the stock number. The others receive it. You have two sensible choices:
- Shopify as the source. Your Shopify inventory is the master and an app pushes its quantities to Amazon. Simple with one warehouse and few channels.
- An inventory management system as the source. Both Shopify and Amazon receive their numbers from a separate system that also handles purchasing, multiple warehouses and other channels. Better once you add a third channel, a second location or bundles.
What you must avoid is two tools both pushing stock to the same listings. They overwrite each other, and the result is worse than no sync at all.
Your Options
| Option | What It Does | Good For | Keep in Mind |
|---|---|---|---|
| Shopify Marketplace Connect | Shopify's own app for listing and selling on marketplaces including Amazon, with inventory synced from Shopify | Shopify centered sellers who want to manage marketplaces from the Shopify admin | Shopify is then the source of truth; check its plan limits and supported marketplaces |
| Amazon Multi-Channel Fulfillment app | Lets Amazon fulfill your Shopify orders from your FBA stock | Sellers whose stock lives mainly in FBA | A fulfillment service, not a full inventory system; check which countries it serves |
| An inventory management system | Pulls orders from both, holds the master pool, pushes stock to both | Several channels or warehouses, bundles, purchasing | Choose one with reconciliation, not just pushes |
| Manual updates or CSV | You adjust each channel by hand | A handful of slow moving products | Breaks down with any volume; oversells are likely |
One historical note: Shopify ended support for its built-in Fulfillment by Amazon fulfillment service on March 31, 2023. Fulfilling Shopify orders from FBA stock now goes through an app, such as Amazon's own Multi-Channel Fulfillment app.
Map SKUs Before Anything Syncs
Mapping is the step that decides whether the sync is right. Each Shopify variant must point at exactly one Amazon seller SKU, and both must point at one product in your source of truth.
| Your Product | Shopify Variant SKU | Amazon Seller SKU | ASIN |
|---|---|---|---|
| Blue mug, 12 oz | MUG-BLU-12 | MUG-BLU-12 | B0EXAMPLE1 |
| Blue mug, 12 oz, fulfilled by Amazon (FBA) | (none) | MUG-BLU-12-FBA | B0EXAMPLE1 |
| Gift set (mug and 2 coasters) | SET-MUG-CST | SET-MUG-CST | B0EXAMPLE2 |
Rules that save you later:
- Use the same SKU on both channels where you can. It makes mapping obvious and reports readable.
- Give FBA offers their own SKU. The same ASIN can have an FBA offer and a merchant fulfilled offer; they hold different stock.
- Map bundles to components. The gift set should reduce one mug and two coasters, not hold its own stock.
- Find the orphans. List Shopify variants with no Amazon match and Amazon SKUs with no Shopify match. Decide each one before you push anything.
FBM and FBA Are Two Different Problems
Fulfilled by Merchant: One Shelf, Two Storefronts
If you ship Amazon orders yourself, Shopify and Amazon sell from the same shelf. This is the classic sync problem: one pool, two channels, and the stock number must reach both quickly. Orders from both channels should reserve units the moment they arrive.
Fulfilled by Amazon: Amazon Holds the Stock
If Amazon fulfills your orders, the units in its network are not on your shelf. Two rules follow:
- FBA stock is not available for Shopify orders you ship yourself. Never add FBA units to the quantity Shopify sees from your warehouse.
- If you want Shopify orders filled from FBA, use Multi-Channel Fulfillment. Then the Shopify listing can draw on FBA stock, and Amazon ships the order. Amazon describes this as one inventory pool serving both Amazon and Shopify orders.
Many sellers run both: FBA for Amazon, their own warehouse for Shopify, and a small FBM offer on Amazon as a backup when FBA runs low.
Try it on your own data: start free, no card needed.
Step by Step Setup
- Clean the catalog in your source of truth: one product per physical item, duplicates merged.
- Count the stock you will sync first, so the starting numbers are true.
- Connect Shopify and Amazon to the tool you chose, with stock pushing turned off.
- Import listings and orders and review the SKU mapping, including orphans and bundles.
- Set up locations: your warehouse, any 3PL and Amazon FBA as separate locations.
- Compare quantities on both channels with your counted stock and decide each difference.
- Set buffers on low stock products for the channel where an oversell hurts most, usually Amazon.
- Turn on stock pushing for a small group of products first.
- Run the test plan below.
- Roll out to the rest of the catalog, then schedule a regular reconciliation.
Which Shopify Number to Sync
Shopify tracks stock in several states. Its Help Center defines on hand as the sum of committed, unavailable and available units, with incoming stock kept separate until it is received. For Amazon you want available: units not already committed to Shopify orders or set aside. Pushing on hand instead would offer Amazon buyers units that Shopify customers already bought.
If you use several Shopify locations, decide which locations' stock may be offered on Amazon. A retail store's back room may not be able to ship Amazon orders on time.
Also check two Shopify settings on every variant you sync: Track quantity must be on, and Continue selling when out of stock should be off unless you deliberately take backorders on your own store.
Prices and Listing Content on Each Channel
Stock should be identical everywhere. Prices and content usually should not be, and that is fine as long as the differences are deliberate:
- Price each channel from its own costs. Amazon's referral and fulfillment fees differ from Shopify's payment fees, so the same margin needs a different price. Keep the gap reasonable: Amazon's Fair Pricing Policy lets it act on prices that are significantly higher than recent prices on or off Amazon.
- Write content for each channel's rules. Amazon has strict title, image and attribute requirements; your Shopify store can tell the brand story at length. Keep the facts (brand, size, materials, barcodes) identical and adapt the presentation.
- Keep one catalog as the source of facts. When a detail changes, change it once and send it to both channels, so they never disagree about what the product is.
Returns and Cancellations
Stock sync is not finished when an order ships. A cancellation on either channel should release its allocation immediately, so the units go back on sale everywhere. A return should come back into stock only after someone has checked it is resellable; until then it belongs in a separate state, not in available. Amazon FBA returns are handled inside Amazon's network, so they change your FBA location's stock rather than your warehouse.
Test Before You Trust It
- Change the stock of a test product in the source of truth and time how long each channel takes to show it.
- Place a real order on Shopify and confirm the Amazon quantity drops.
- Place or simulate an order on Amazon and confirm the Shopify quantity drops.
- Cancel one of those orders and confirm the stock comes back on both.
- Sell a bundle and confirm its components drop on every listing that sells them.
- Set a product to zero and confirm it shows as out of stock, not as an error, on both channels.
- Confirm that FBA stock does not appear in the quantity Shopify sells from your warehouse.
Troubleshooting
| Symptom | Likely Cause | Fix |
|---|---|---|
| Amazon shows more than you have | On hand pushed instead of available, or FBA units counted | Push available only, keep FBA as its own location |
| A sale on one channel does not reduce the other | SKU not mapped, or the two listings mapped to different products | Map both listings to the same product |
| Quantities flip back and forth | Two tools pushing stock to the same listing | Disconnect one; keep a single source of truth |
| Bundle sold, components still show the old stock | Bundle stocked on its own | Define the bundle by its components |
| Shopify keeps selling at zero | Continue selling when out of stock is on | Turn it off for that variant |
| Numbers drift slowly over weeks | Manual edits on a channel, or rejected updates | Run a reconciliation and stop editing on the channel |
How Invechar Syncs Shopify and Amazon
Invechar connects to Shopify and Amazon and imports products, orders, costs and stock. Both channels then sell from one master pool: orders from either allocate stock the moment they arrive, and the available number pushes to your linked listings as it changes, with a safe Shopify sweep every three hours. A drift check on the same schedule compares Shopify and Amazon with the pool, and any difference becomes a task you approve, with automatic pushes paused for that product until you decide. Your Amazon FBA stock is its own location and never counts as sellable on Shopify, bundles draw down their components, and when you first connect, stock pushes stay blocked until you have reviewed the import's differences, so nothing is overwritten. Tracking from shipped orders goes back to the channel that sold them.
See how to connect Shopify and connect Amazon, read about stock sync and drift checks, browse all integrations, or start with the complete multichannel inventory guide.
Sources
- Shopify Help Center, Inventory states. Accessed October 8, 2026.
- Shopify Help Center, Fulfillment by Amazon, on the end of the built-in FBA fulfillment service. Accessed October 8, 2026.
- Shopify Help Center, Selling out of stock products. Accessed October 8, 2026.
- Shopify App Store, Shopify Marketplace Connect, and the Shopify Changelog, Shopify Marketplace Connect. Accessed October 8, 2026. Supported marketplaces and plans change; check the listing.
- Amazon Supply Chain, Multi-Channel Fulfillment app for Shopify. Accessed October 8, 2026.
- Amazon Seller Central Help, Amazon Marketplace Fair Pricing Policy (sign in required). Accessed October 8, 2026.