Shopify and Amazon FBA: A Guide to Automating Fulfillment Between Your Amazon and Shopify Stores

Rick Wong 4 March 2021

For intermediate Amazon sellers who have been seeing traction in their sales on Amazon and familiar with running an Amazon store, the next logical step will inevitably be growth. Shopify and Amazon FBA might seem like rivals at first glance, but why not use both?

Remember, there are two roads that Amazon sellers will venture into if they are looking to grow their business: 1) Start selling on other Amazon marketplaces, and 2) Set your online store. In this article, we will talk about the former. 

In setting up an online store, Shopify is a prevalent option due to the simplicity of use, integration with payments, and the number of nicely designed responsive themes. 

This article will assume that you have a Shopify store set up already.

Why Shopify for Amazon Sellers?

Collection of Customer and Behavioral Data

One of the main cons of selling on Amazon is the lack of data. In Amazon, you cannot collect any customer-related data. So that means you won’t get certain customer information such as their email address and phone numbers. On Shopify, you will see the customer’s email address and which channel they found your product (Google/Facebook).

Shopify also allows for third-party pixels, which will enable you to track the customer journey and behavior on your website. Using these 3rd party pixels enables you to retarget your potential customers in a very customizable fashion. This will not be possible in the Amazon marketplace.

Building a Brand

If you want to market your product off Amazon, you need a custom website to convey your brand or your product message. These include any videos, photos, messaging, or customer support. None of which can be added to create a much more structured Amazon product listing page.

A more practical example is, let’s say you are promoting your line of products for your pop-up store, the most brand-friendly way to do this is to advertise your own online store URL address than displaying an listing.

Cashflow is Better on Shopify

Another reason to use Shopify for your Amazon store is cashflow. One big issue for Amazon sellers is that Amazon withholds payment for 14 days, and if you are a high-growth business, you will run into a cash crunch very quickly. That is why there has been a proliferation of Amazon-specific lenders catering to this space. 

On the other hand, Shopify allows for payment gateways such as Stripe and Paypal. These payment gateways settle payments in 4 days or less. In the case of Paypal, you will get the payment almost immediately. By getting cash in your bank account quicker, you can meet any inventory or operational needs that require money instead of looking for external financing.

Cheaper Transaction Fees

Shopify transaction fee is 2.9%, while the Amazon transaction fee is 15%. Enough said there.

Why Should You Integrate your Amazon and Shopify Stores?

To run your online business as lean and as efficiently as possible, you need to look for ways to automate and leverage technology as much as possible. One such example is leveraging Amazon advertising software to optimize and automate the time-consuming Amazon PPC optimization processes.

In running both Amazon and Shopify stores, you want to avoid as much as possible to be doing duo work where you don’t need to. A prime example of this would be product listing creation and fulfillment. If you were to add a new product, you don’t want to be, first, listing on your Amazon seller central, and second, manually creating the same listing on Shopify.

What are You Integrating?

Between Amazon and Shopify, Shopify already has a feature where you can automate the fulfillment between your Shopify store and Amazon FBA. That means you can automatically fulfill your Shopify order via Amazon FBA without having to go to Amazon seller central, then go to multi-channel fulfillment, and finally having to enter the customer’s address manually and click ship. This doesn’t seem like much, but imagine having to do this for 20+ orders daily; then it will quickly become a much-needed time saver!

Requirements to Integrate Shopify with Amazon for Fulfillment

  1. You have a seller account with Amazon using Amazon FBA.
  2. You have, at a minimum, a basic subscription tier on your Shopify Store.
  3. Selling on Amazon US or Canada marketplaces only.
  • Please note* →  Before integrating you need to make sure your Shopify store currency matches the location of your Amazon marketplace/FBA country. For example, if your store currency is CAD, then the integration will only fulfill from the Amazon FBA CA warehouse and only to a Canadian address. If your Amazon marketplace account is for another region, then you need to use a third-party app for fulfillment integrations.

Step by Step Integration

1. Activate Fulfillment by Amazon

You will need to first integrate your Shopify account with your Amazon account by doing the following steps:

A. Use this link to sign in to your Amazon Seller Central account.

B. On the Marketplace Web Services or MWS page (above), read the terms and conditions, click “next.”

C. Continue the process by clicking “Continue” and you will be brought back to the Shopify shipping settings page.

2. Match shipping rates and settings between Shopify and Amazon FBA

Since you are at the end of the day using Amazon FBA to make the final last-mile delivery, your service levels and rates need to match exactly that of Amazon FBA. 

Amazon FBA offers 3 tiers of shipping service, and they are:

  • Standard Shipping
  • Two-Day Shipping
  • One-Day Shipping

Back to the Shopify settings screen, go to the “Shipping” section and then click “Manage Rates.”

Since we need to match shipping information based on your Amazon FBA settings and country, you will delete all the default shipping rate and shipping zones info that not the country where your Amazon FBA is based.

Once all the above is cleared, you will add back the shipping tiers that Amazon FBA supports (Standard Shipping, Two-Day Shipping, or One-Day Shipping), by clicking on “Add Rate” (see above). 

When adding the rates, make sure the rate name is exactly as they appear on Amazon FBA.

  • Standard Shipping
  • Two-Day Shipping
  • One-Day Shipping

To find your price for the above tier, you can find the cost to fulfill via Amazon for your products tier here

An example, my product size tier is “Small standard: 10 to 16 oz.” The price I would input would be:

  • Standard Shipping $5.79
  • Two-Day Shipping → $5.89
  • One-Day Shipping → $12.80

Once you are done adding your 3 shipping rate names and their corresponding prices, click “save” at the bottom of the page.

3. Add a New Product on Shopify

Now you will add a new product listing on Shopify, which will also match your listing on Amazon, the primary field used to link the listing between platforms will be the “SKU” field. More on that later.

To add a new product, go to the “Product” on the left nav bar and click “Add product.”

Once on the product listing edit screen, scroll down to the “Inventory” section, and under the “Inventory managed by” select “Amazon Marketplace Web” in the dropdown. In this section, make sure to enter the SKU field, which exactly matches the corresponding Seller SKU in Amazon. 

Also, don’t forget to add and match the correct values for the weight, title, price, and other product listing information on this page.

4. Fulfill Your Shopify Order via Amazon FBA

Now for the final step, once you get an order, click on the “All Orders,” then click on an order # that is unfulfilled.

On the next screen, you will click “Request Fulfillment.”

Choose the shipping method under the drop-down menu that matches the customer selection (arrow #1), then click on the button “Fulfil Items.”

You will now see that this order number’s status has changed to “Pending Fulfillment” and its corresponding order on Amazon Seller Central.

You can also see an audit of the exact flow of fulfillment on the order page’s bottom portion. If the order has been successfully requested, there will be a line that will say “You requested fulfillment of x items from amazon_marketplace_web”.

Once Amazon FBA actually ships and fulfills this order, this integration will automatically update the fulfillment status to “Fulfilled,” and add the tracking number to the order page as well.


That concludes how to integrate the fulfillment process between Shopify and Amazon stores. In the ever more competitive E-Commerce space, multi-channel selling is as essential as ever. Therefore Shopify stores, with its supported apps and integration, have been very popular amongst Amazon sellers.

It can be time-consuming running a Shopify store co-currently with your Amazon FBA business, but integrations and tools such as the above make running both platforms much easier and less time-consuming. Continue and find ways to automate your platform’s operations and your E-Commerce brand will be ready to scale to new heights!

If you have questions or insights to share, please feel free to post them via the comments section. Please also consider joining our Facebook Group where we discuss any questions you may have about running an Amazon business.

We are SellerMetrics, our Amazon PPC Software helps Amazon sellers, brands, KDP Authors and agencies navigate Amazon Advertising PPC via bid automation, bulk manual bid changes, and analytics.




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