How to Set Up FBA Inventory Sync

Your FBA stock lives in Amazon's warehouses. Your Shopify and eBay listings need to reflect it accurately. Here's how to make that happen.

How FBA inventory works and why sync is complicated

Fulfillment by Amazon (FBA) means your products are physically stored in Amazon's fulfillment centers. When a customer orders on Amazon, Amazon picks, packs, and ships the item. You don't touch the fulfillment at all.

This is excellent for Amazon sales velocity. FBA products get Prime eligibility, which dramatically increases conversion rates, and Amazon handles shipping speed, customer service for logistics issues, and returns processing.

But here's where it gets complicated for multi-channel sellers: your FBA inventory is not your Shopify inventory, your eBay inventory, or your Etsy inventory. They are physically separate stock locations.

If you have 50 units of a product in an Amazon fulfillment center and 20 units in your own warehouse, a Shopify sale should draw from your warehouse stock. An Amazon sale draws from FBA stock. If you mistakenly show the same 50 FBA units on your Shopify store and an eBay listing, you could "sell" inventory that was never available for those channels to fulfill.

FBA vs. FBM inventory: two separate pools

Understanding this distinction is the foundation of FBA inventory sync.

Inventory type Physical location Who fulfills Amazon orders Who fulfills Shopify orders
FBA stock Amazon fulfillment center Amazon automatically Can use MCF (see below) or NOT this stock
FBM / own stock Your warehouse/home You ship manually You ship manually

The key point: FBA stock and your own warehouse stock are separate. You cannot use FBA stock to fulfill a Shopify order without explicitly routing it through Amazon's Multi-Channel Fulfillment (MCF) service.

Most FBA sellers maintain two pools: FBA stock that exclusively serves Amazon orders, and local stock that serves their other channels. The sync challenge is ensuring each pool's levels are accurately reflected on the right platforms.

Using FBA for orders from Shopify and eBay (MCF)

Amazon offers Multi-Channel Fulfillment (MCF), a service that lets you use your FBA inventory to fulfill orders from non-Amazon channels, including Shopify and eBay. Amazon ships the order from your FBA stock on your behalf.

MCF is convenient because it means one inventory pool can serve multiple channels without managing your own warehouse. The tradeoff is cost: MCF fees are higher than standard FBA fulfillment fees, and shipments arrive in Amazon-branded packaging (unless you pay for blank box service), which can look odd for buyers who ordered from your Shopify store.

If you use MCF, your FBA stock count becomes your shared pool across all channels. This simplifies inventory math but increases your per-fulfillment cost and creates an Amazon dependency for all your channels.

If you don't use MCF, your FBA stock is Amazon-only, and you maintain separate local stock for other channels. This is the more common approach for established multi-channel sellers.

Setting up FBA inventory sync with Commerce Kitty

Commerce Kitty handles FBA inventory in two ways depending on your setup: MCF mode (one shared pool) or split-pool mode (FBA stock and local stock tracked separately).

1

Connect Amazon Seller Central

In Commerce Kitty, connect your Amazon account through the "Add Channel" flow. Commerce Kitty requests read access to your FBA inventory levels through the Selling Partner API.

2

Connect your other channels

Connect Shopify, eBay, Etsy, or any other platform you sell on. Commerce Kitty imports your product catalog from each channel.

3

Configure inventory source per product

For each linked product, specify whether non-Amazon channels should reflect FBA stock (MCF approach) or your separate local stock. This configuration tells Commerce Kitty which inventory number to broadcast to which channel.

4

Set FBA replenishment thresholds

Configure alert thresholds for your FBA stock. When available FBA units drop below your threshold, Commerce Kitty alerts you to prepare a replenishment shipment to Amazon.

5

Verify sync accuracy

After setup, compare inventory counts in Commerce Kitty with your Amazon Seller Central FBA inventory report and your Shopify/eBay inventory counts. They should align. If they don't, check for unlinked products or pending orders.

Managing FBA replenishment and reorder triggers

Running out of FBA stock is more damaging than running out of local stock. When your FBA inventory hits zero, your Amazon listings go inactive. Your Buy Box goes away. Your search ranking drops as your listing accumulates zero-sale days. Rebuilding takes time and lost rank is slow to recover.

Set reorder points, not just zero-stock alerts

A zero-stock alert is useless for FBA because by the time you receive it, create a replenishment shipment, and ship it to Amazon, your listings could be inactive for weeks. Amazon's replenishment timeline typically runs 2-4 weeks when you factor in shipment creation, transportation, and check-in at the fulfillment center.

Your reorder point should be: (average daily sales) x (replenishment lead time in days) + safety stock. If you sell 10 units per day and replenishment takes 21 days, your reorder point is 210 units plus whatever safety buffer you're comfortable with.

Track sell-through rate by channel

If you use FBA stock for multiple channels (MCF), track which channel is consuming inventory fastest. A sudden spike in Shopify orders drawing from FBA stock can accelerate depletion faster than your replenishment schedule accounts for. Commerce Kitty's channel-level sales data helps you spot these patterns before they become stockout events.

Dealing with stranded and suppressed FBA listings

FBA inventory sync breaks down in a specific scenario: stranded inventory. Stranded inventory is FBA stock that is at Amazon's fulfillment center but not associated with an active listing. You're paying storage fees but not selling.

This happens when a listing is deleted or deactivated while the inventory is still at Amazon, when a listing is suppressed due to a policy violation, or when pricing settings trigger automatic deactivation. From Commerce Kitty's perspective, stranded inventory exists in Amazon's system but generates no sales activity.

Check your Amazon Seller Central FBA inventory report weekly for stranded units. The Inventory Performance Dashboard in Seller Central highlights stranded inventory and suggests fixes. The fix is usually re-listing the ASIN or creating a removal order if the inventory is unsellable.

Frequently asked questions

Can I show my FBA stock count on my Shopify store?
Yes, if you're using MCF for Shopify orders. In that case, your FBA stock is the inventory available for Shopify fulfillment, and Commerce Kitty reflects that count on Shopify. If you're NOT using MCF and fulfill Shopify orders from your own warehouse, Shopify should show your local stock count, not your FBA count.
What's the difference between FBA available units and total units?
Amazon tracks several FBA inventory states: available (ready to sell), reserved (allocated to pending orders or transfers), inbound (in transit to Amazon's warehouse), and unfulfillable (damaged or unsellable units). Commerce Kitty syncs your "available" count to other channels, not your total FBA count, to avoid showing inventory that isn't actually ready to fulfill orders.
How often does FBA inventory update?
Amazon's Selling Partner API provides near-real-time inventory updates for fulfilled orders. FBA inventory levels in Commerce Kitty reflect Amazon's available count within minutes of a sale. Inbound shipments typically update within a few hours of check-in at Amazon's fulfillment center.
What happens to my eBay and Shopify listings when FBA stock hits zero?
If you're using FBA stock as the inventory source for Shopify and eBay (MCF approach), Commerce Kitty will set those channels to zero/out-of-stock when FBA available units reach zero. This prevents overselling but does deactivate your listings on those channels until FBA stock is replenished.
Is MCF worth the extra cost?
It depends on your volume and alternative fulfillment costs. MCF fees are typically $3-8 per unit depending on size, higher than standard FBA fees but potentially competitive with your own shipping costs especially for heavier items. The convenience of one inventory pool is real. Run the numbers for your specific product mix before committing to MCF as your multi-channel strategy.

For broader setup, see connecting Shopify to Amazon Seller Central and expanding from Shopify to Amazon.