Shopify & Amazon Integration : how can i link only 1 SKU to Amazon for fulfillment?

Technical Q&A

Topic summary

A merchant is transitioning from Amazon FBA to a 3PL partner for 4 out of 5 SKUs, keeping only their best-selling SKU on FBA. The core problem: FBM (Fulfilled By Merchant) orders from Amazon are syncing to both the 3PL directly and to Shopify, creating duplicate orders at the 3PL.

Current Setup:

  • 1 SKU remains FBA (also sold on Shopify website)
  • 4 SKUs now FBM, fulfilled by 3PL
  • 3PL integrated with both Amazon and Shopify
  • Amazon Sales Channel cannot be fully disabled due to the FBA SKU

Attempted Solutions (unsuccessful):

  • Removed Amazon Sales Channel from the 4 FBM product listings
  • Changed inventory management to Shopify for those 4 SKUs

Suggested Approaches:

  • Replace Amazon Sales Channel with Amazon Fulfillment Service for more granular control
  • Use third-party apps (Codisto for FBM order import, Order Automator for automation)
  • Manage listings separately: Shopify admin for website, CSV uploads for Amazon Seller Central
  • Configure SKU mapping and order-routing filters in integration apps to prevent FBM order duplication
  • Consider Amazon MCF or Buy with Prime apps to isolate FBA fulfillment to the single SKU

Status: Multiple users report similar issues; discussion remains open with no confirmed resolution.

Summarized with AI on October 24. AI used: claude-sonnet-4-5-20250929.
1

Hi Community!

I have searched in the forum but cannot find the answer, hopefully, someone can guide me.

  • For the last 5 years, we were primarily an Amazon Seller, selling FBA only and all our Shopify orders were FBA as well.
  • We are moving away from FBA as we had a lot of issues with Amazon FC this year.
  • We have 5 SKUs, 1 one of them (our best seller on Amazon), will for now stay FBA.
  • The other 4 SKUs are now fulfilled by our 3PL partner and are market FBM (Fulfilled By Merchant) in Amazon.
    • The 3PL is fully integrated with Amazon and Shopify.
    • Meaning all Amazon orders for the 4 FBM SKUs go straight from Amazon to the 3PL.
    • However, here is the issue: those Amazon orders also arrive in Shopify! It means that they show twice at our 3PL
  • The 5th SKU that is FBA is also sold on our website (and FBA), meaning I cannot fully deactivate the Amazon/Shopify integration
  • The question is: how to have 1 SKU out of the 5 linked to Amazon only?

I have taken out the Amazon Sales Channel in each of the 4 Shopify Listings but it has not solved the issue.

I have also made sure that for those 4 SKUs the inventory is managed by Shopify and not by Amazon anymore.

In theory, those 4 SKUs should not be linked but it seems that it is not enough to solve the issue.

Pretty sure we are not the only ones to have this need :slightly_smiling_face: Hopefully, someone has the answer.

Thank you very much for your help.

Valerie

BetterThanCoffee.com

2

I’ve had problems with the Amazon Sales Channel in the past so stopped using it completely.

Instead I do this (on a store that has both Shopify orders to be fulfillled by Amazon FBA, and also Amazon orders to be fulfilled FBM):

  1. Use the Amazon Fulfillment Service instead (https://help.shopify.com/en/manual/shipping/fulfillment-services/amazon).

  2. Configure the product(s) you want to fulfill by Amazon. (you can also automate the fulfillment if you want, using Order Automator app, details here: https://speedboostr.com/automate-order-fulfillment-on-shopify/).

  3. Manage the product listing on Shopify via the Shopify admin, and for Amazon via CSV (in seller central: Inventory > Add products via upload).

  4. For importing FBM orders from Amazon, into your Shopify store, I use the app Codisto.

This system essentially keeps Amazon and Shopify listings separate, except for fulfilling the items you choose to be fulfilled by FBA, and importing FBM orders.

3

Hi,

Did you find solution to your issue? Now I am facing same problem - I do not understand why my FBM orders from Amazon shows in Shopify orders tab. And also- to make it more complicated Amazon shows this order as shipped and Shopify as fulfilled even if nobody did anything with the order. How is it possible? I hope you found an answer by now :).

I also do FBA for most of my SKUs and for items sold in www (shopify) so I can not disconnect Amazon from shopify..

Thanks

Ewa

4

To keep just one Shopify SKU fulfilled by Amazon FBA while managing the rest through your 3PL without creating duplicates, you need to match the SKU code in Shopify to the corresponding Amazon FBA SKU listed in Seller Central. Then, you map this SKU in your Shopify-Amazon integration app.

You must remove any FBA mapping for other SKUs. Set Shopify or your 3PL as the one controlling the inventory, and make sure there’s no link to Amazon MCF. Use the integration’s order-routing options or filtering tools to prevent FBM orders from syncing to Shopify more than once. Apps like Amazon MCF (Multi-Channel Fulfillment) or Buy with Prime can help isolate FBA fulfillment to just the single SKU.