Updated September 8th, 2022

I don’t know about you but I’m ALWAYS looking for ways to automate tasks and save time.

This guide is about automating order fulfillment on your Shopify store.

Here I’ll show you:

Even if you don’t sell on Amazon you can still use FBA. If you haven’t sold on Amazon yet join the party it’s an easy additional revenue channel! πŸ’°πŸ’΅

If you sell on Amazon and don’t have a website yet, check this Shopify Setup Tutorial to create a Shopify store and establish a home base + additional sales channel.

Who is this post for?

a) If you are manually fulfilling Shopify orders and want an automated solution.

b) If you currently sell on Amazon FBA and want to fulfill Shopify orders using your FBA inventory.

c) If you want some ideas on how to run the fulfillment side of your business more efficiently.

Fulfillment Services

As a former Shopify store owner, I’ve used a few fulfillment solutions but so far Amazon has turned out to be the most reliable + best price model.

The other 3rd party fulfillment services I’ve used were either too expensive or just not good.

Side note: Shopify Fulfillment Network

Shopify has their own Shopify Fulfillment Network you can check out here: shopify.com/fulfillment.

I haven’t used it yet but last time I checked you can sign up for it if you’re doing 10+ orders a day.

What is Amazon FBA vs Multi-Channel Fulfillment?

Amazon FBA: Orders placed on Amazon and fulfilled by Amazon.

Amazon MCF: Orders fulfilled by Amazon (FBA) but placed anywhere outside of Amazon.

Both are FBA but specifically Amazon MCF allows you to ship inventory directly to Amazon warehouses and use their network to fulfill your Shopify (and other channel) orders.

Here’s how Multi-Channel Fulfillment works:

amazon multi-channel fulfillment how it worksSource: Amazon MCF

MCF is easy, low cost, and efficient. It also allows you to sync your Shopify inventory with your Amazon warehouse inventory.

You can see Amazon pricing here.

MCF is available in these marketplaces:

  • USA
  • Canada
  • Mexico
  • UK
  • Germany
  • France
  • Italy
  • Spain
  • Japan

How to automatically fulfill Shopify orders with Amazon FBA

Here’s an overview of the steps required:

  1. Register an Amazon Seller Central account and upload products
  2. Install a Shopify app that’s a registered Amazon Selling Partner Developer
  3. Configure your shipping rates
  4. Configure your FBA products in Shopify
  5. Create a plan for international orders

1) Register an Amazon Seller Central account and upload your products

If you don’t have an Amazon Seller Central account go to sellercentral.amazon.com to get started. You can also see all available marketplaces here.

After you have an account you can upload your product listings to Amazon.

2) Install a Shopify app that’s a registered Amazon Selling Partner Developer

I recommend Order Automator, here’s why:

  • It has excellent reviews
  • The team has US based developers that understand eCommerce and constantly build new features on request
  • The app founder (me :D) is a 10+ year Shopify developer and started, managed, and sold a Shopify store that also had a presence in multiple Amazon marketplaces.

Order Automator shopify app that connects to amazon

After installing the app, go to Auto Fulfill then click on the Amazon FBA tab and follow the instructions to connect to your Seller Central account.

3) Configure your shipping rates

Amazon offers these shipping rates:

  • Standard (3-5 business days)
  • Expedited (2 business days)
  • Priority (1 business day)

See more details at MCF Shipping and Packing FAQ

You can map your Shopify shipping methods to Amazon’s methods in Order Automator:

Pro tip: To show more info about shipping methods you can edit your “theme language” on the checkout page like this:

  1. Go to Online Store > Themes
  2. On your theme, select Actions then Edit languages
  3. Select Checkout & System
  4. Edit the Shipping method notice field

Edit Shopify checkout shipping text

Now your checkout page will show that custom text:

Shopify checkout page shipping edit

4) Configure your FBA products in Shopify

With Amazon connected and the feature in Order Automator enabled, you can now go to the product(s) you want to sync / fulfill and change Inventory managed by to FBA by Order Automator.

If your Shopify SKU matches the Amazon SKU exactly, then no further action is needed. If the SKUs are different, you can map those SKUs in Order Automator. You can even map product bundles. πŸ‘

Tracking and fulfillment: When new orders come in with line items that are managed by FBA by Order Automator, the order will automatically get created in Amazon. Order Automator routinely pings Amazon to check the status of these orders, and after they’ve shipped updates the tracking in Shopify and marks the line item fulfilled.

5) Create a system for international orders

As of this writing MCF only supports international fulfillment for media products (books, music, videos, and DVDs).

For all other products you’ll need a backup plan.

International fulfillment options:

  • Ship in-house
  • Connect multiple Amazon marketplaces
  • Use another 3rd party fulfillment service

You can decide what’s best for your business, but here’s an idea:

  • Set up an Amazon FBA account in any country that you do regular order volume
  • Use Order Automator to request fulfillment to the respective country
  • For countries that you don’t do many sales in, ship those in-house

It would be awesome if Amazon opens up international MCF fulfillment – let them know you would like this feature, maybe your request will be the tipping point and they will make it happen. ✊

For more details about Amazon FBA with Shopify or any feature of Order Automator, see the Order Automator FAQ page here.

Pros and Cons of fulfilling Shopify orders with Amazon


  • automated shipping solution
  • Amazon warehouses work 24/7 and ship fast
  • inventory syncing with Shopify and Amazon
  • low cost


  • no control over package branding (yet)
  • Amazon MCF doesn’t ship international (yet)
  • Amazon decides where to ship from, so 1 order may receive multiple shipments from different warehouses

Unbranded packaging and international shipping are in beta, according to this page (screenshot here in case you don’t have a seller central account).

unbranded packaging for amazon fba

Custom Auto Fulfillment

On a related note, if you simply need to mark line items fulfilled, automatically, based on the product or order conditions, you can use Order Automator to handle that too.

Here’s how:

  1. Create a custom fulfillment rule on the Auto Fulfill page
  2. When a new order comes in the app will mark line items fulfilled that match the conditions you created

Need help?

If this guide doesn’t work for your situation, or you want to make a feature request, contact Order Automator app support to get dialed in.

Cheers to automation! ✊