Linking Shopify to Amazon: How to Sync Your Stores in 2026

Managing an Amazon and Shopify store at the same time can turn into a headache fast. You update a variant in one place but forget to fix it in the other, your inventory tracking gets out of sync, and orders keep stacking up in two different dashboards. Before long, you’re spending more time jumping back and forth between Seller Central and your Shopify dashboard than actually running your business.

That’s why so many sellers look into linking Shopify to Amazon. Once you have both platforms connected, your catalog stays consistent, your inventory syncs automatically, and your orders become a whole lot easier to manage. Even though you’re still selling on both platforms, the amount of hassle and day-to-day work becomes much more manageable.

In this guide, I’ll walk you through your options for connecting Shopify and Amazon. We’ll talk about the tool most sellers use in 2026, common mistakes to avoid, and I’ll go over each step one by one. By the end, you’ll have all of the info you need to choose the right integration app and successfully link your two sales channels.

Why Connect Shopify to Amazon?

Linking Shopify to Amazon gives you a more stable, predictable business because you’re no longer relying on a single sales channel. While Amazon is unmatched for traffic, you are entirely at the whim of Amazon’s policies. Changes to the search algorithm, new fees, or policy updates can potentially destroy your business overnight. Expanding to Shopify gives you more control over your brand and better peace of mind. When both platforms work together, you get access to millions of Amazon shoppers while still growing your brand independently on Shopify.

If you already sell on both Shopify and Amazon, one of the biggest advantages of linking them is a unified inventory. When your catalog syncs between both platforms, you avoid overselling, mismatched counts, and manual stock updates that are prone to mistakes. This can be even more of an issue as your business grows and you hold inventory in multiple locations.

There’s also a major time-saving benefit. Instead of constantly updating two sets of listings or managing orders across two separate dashboards, your catalog, pricing, and orders stay centralized. This can save you several hours each week, as your business grows and the orders pile up.

And as I touched on already, if you’re an Amazon seller, adding Shopify as a sales channel lets you grow outside of Amazon’s algorithm. With Shopify, you own the customer relationship. You can create email campaigns, build relationships with repeat buyers, and work on long-term brand building. This is critical if your goal is to develop a brand that stands the test of time.

Finally, you’ll also have the option of using Amazon’s Multi-Channel Fulfillment to ship orders from your Shopify store using your FBA inventory. This can be another way to simplify your business and cut down the time you spend dealing with inventory management.

What You’ll Need Before Connecting Shopify to Amazon

Before you can start connecting Shopify to Amazon, you’ll want to make sure you have everything you need. This means verifying that you have a Professional Seller Account on Amazon and that you’ve set up your Shopify catalog so it’s ready to be synced. Let’s go over these steps now.

Amazon Account Requirements

Your first requirement is to have an active Amazon Professional Seller Account. The Individual plan doesn’t support the tool required for catalog syncing or multichannel order routing, so the Professional plan is your only option here. If you currently have an Individual plan, you can easily upgrade to a Pro one in Seller Central.

Along with the ability to link to Shopify, the Pro plan also comes with a ton of other benefits, like the Brand Registry, Amazon Ads, seller incentive programs, the ability to get ungated, and more. If you’re serious about selling on Amazon, I highly recommend the Pro plan, regardless of whether you plan to sell on other platforms or not.

To learn more about the Professional Seller account and the process of signing up to sell on Amazon, check out our guide: How to Create an Amazon Seller Account in 2026.

Shopify Catalog and Operational Requirements

Next, you’ll want to make sure that your Shopify product catalog is fully organized before connecting it to Amazon. Variants, SKUs, and parent-child relationships need to be correct because the two platforms organize product data differently. From my own experience, as well as other sellers I’ve talked to, the most common errors happen when your Shopify product variants don’t cleanly map to Amazon’s parent-child ASIN setup.

Matching SKUs across both platforms is also important. All integration apps rely on the SKUs to sync inventory and to identify the corresponding listing. It’s worth double-checking this before you start syncing, or you’ll end up spending time removing duplicates and manually adjusting the app’s product mapping suggestions.

You should also make sure that your inventory tracking is accurate and your Shopify listings are up to date. It might sound like extra work, but a clean starting point can reduce the risk of errors and make it easier if you decide to set up MCF shipping for your Shopify orders at a later date.

Choosing the Right Shopify–Amazon Integration App

Once you’ve got everything ready, you’re next step is deciding which integration app to use. The right app depends on how many products you sell, how complex your business is, and whether you only care about linking Shopify and Amazon, or you plan to expand to other marketplaces later.

In my opinion, this decision comes down to choosing the native Shopify Marketplace Connect app or a third-party tool.

Shopify Marketplace Connect

Marketplace Connect is the most popular option for sellers because it’s directly supported by Shopify. The app lets you link products, sync inventory, and push new listings to Amazon without learning a separate system. The setup is quick, and it’s free for up to 50 orders each month.

I recommend Marketplace Connect if you’ve got a small to mid-sized catalog and want a simple connection that keeps your listings and inventory aligned. If your products only have a few variants, things usually sync without much trouble. Just keep in mind, from my own experience, if you have a large catalog or a lot of complex parent–child ASINs, you’ll most likely need to spend some time cleaning up your product data before everything works as expected.

For most sellers, the free tier and the fact that the app is fully supported by Shopify make it an easy choice and by far the most popular option.

When to Use a Third-Party Integration App

For sellers with a larger catalog or businesses with multiple sales channels and marketplaces, Shopify Marketplace Connect can be a bit limiting. This is where third-party tools like CedCommerce, LitCommerce, and CS Amazon Integration come in. Each of these tools offers more flexibility and control compared with the alternative.

I won’t go over each one in detail, but here’s a quick breakdown:

• CedCommerce: A good fit if you have a large or variation-heavy Amazon catalog and need the ability to adjust attributes, categories, and pricing rules.
• LitCommerce: Helpful if Shopify is your main store and you want to expand your business out to Amazon, eBay, Etsy, Walmart Marketplace, and other platforms without rebuilding everything from scratch.
• CS Amazon Integration: Best for sellers active in several Amazon regions who need reliable syncing across different countries and currencies. Available in the Shopify app store.

Compared with Marketplace Connect, each of these tools will require a bit more setup. They each use their own dashboards, templates, and automation rules, so there can be quite a bit to learn. However, in exchange, they can handle large catalog sizes and complicated edge cases much better than Marketplace Connect. If you’ve only got a small number of SKUs, these tools are probably not worth it, but for larger businesses, they are well worth a look.

How to Link Shopify to Amazon (Step-by-Step)

As I just mentioned, Shopify Marketplace Connect is the most common method used to link Amazon and Shopify, and is also the method I recommend for most sellers.

In this section, I’ll walk you through the exact steps to set up Marketplace Connect so you can get everything linked up without any issues.

Step 1: Install Shopify Marketplace Connect

To get started, head over to the Shopify App Store and search for “Shopify Marketplace Connect.” Click on the app and install it on your Shopify store.

The pricing information is listed on the app page, but to be clear: your first 50 marketplace-synced orders each month are free, and anything beyond that is charged at 1% of order volume, capped at a maximum of $99/month.

Step 2: Connect Your Amazon Seller Central Account

Next, open Marketplace Connect from the Apps menu and click Connect Amazon. Then pick the region where you sell, such as Amazon.com or Amazon.ca. If you sell in more than one region, you can add those later as separate connections.

You’ll be prompted to log in with your Amazon Seller Central credentials and grant permission for Shopify to talk to your Amazon account. If your business name, address, or tax information looks different between Shopify and Amazon, Amazon may flag the connection for a quick review. For this reason, I recommend double-checking your details ahead of time to save you any potential hassle or delays.

Step 3: Link Your Existing Product Listings

Once you’ve linked the two accounts, Marketplace Connect scans your catalog and groups products based on how well they match your Amazon listings. Your products will be separated into three categories:

• Ready to List: SKUs or GTINs that are a clean match between Shopify and Amazon
• Close Match: Listings that most likely match, but there may be small errors or discrepancies.
• No Match: The app couldn’t find a match for the product.

For products listed in the Close Match group, you’ll need to take some time to look at each potential match. Most of the time, there will be a minor issue with a variation, so pay close attention to things like size, color, and style to make sure they line up before approving them.

After you’re satisfied that the listings match up, click Link Listings. You can watch the sync in the Listings tab, where each product will display a status showing if the listing is active, pending, or needs more information.

Step 4: Create New Amazon Listings from Shopify (Optional)

If you sell products on your Shopify store that you haven’t listed on Amazon yet, Marketplace Connect lets you publish them straight from your Shopify admin. To do so, go to the Listings tab, choose a product that is not linked, and fill in the required Amazon fields such as category, title, images, and attributes.

Just keep in mind that you’ll need to make sure that everything follows Amazon’s listing rules. For example, your images must meet Amazon’s size requirements, your title has to use the correct format and length, etc. Depending on your product category, you may also need to fill out extra information, like compliance or ingredient information.

Once everything looks good, publish the listing and give Amazon some time to process it. Standard items tend to get listed right away, while restricted or sensitive categories can take longer as they need to get approved first.

Using Amazon MCF With Your Shopify Store

If you already use FBA in your Amazon business, Multi-Channel Fulfillment can be a great way to ship your Shopify orders without having to deal with another warehouse or 3PL. MCF lets you fulfill orders for Shopify with the same inventory you are already using for Amazon.

Getting started only takes a few minutes. You’ll enable MCF inside Seller Central, install an MCF-compatible Shopify app, connect your account, and map your SKUs so the app knows which Shopify products match your FBA items. Once everything is set up, you can send orders to Amazon automatically or choose to approve them manually before fulfillment.

Pricing for MCF is usually a little higher than FBA, but it’s still based on your product’s weight and size. You can choose between two delivery speeds: Standard, which takes about three business days, or Expedited, which arrives in two business days but typically costs around three dollars more per item.

While MCF isn’t required to link Amazon to Shopify, I thought it was worth pointing out. Depending on your business and your own goals, adding MCF to your Shopify store can be a great way to guarantee fast shipping speeds and make your inventory management a lot easier.

For more information on MCF and how you can take full advantage of Amazon’s powerful fulfillment network, check out my guide to Supply Chain by Amazon.

FAQs About Linking Shopify to Amazon

Should You Link Shopify to Amazon?

In my opinion, if you’re an Amazon seller with a Shopify store, there is really no downside to linking Shopify to Amazon. When the two platforms are connected, you get consistent inventory tracking, organized order syncing, and you are not stuck jumping back and forth between Seller Central and your Shopify dashboard.

The method you choose depends on your business and what matters most to you. Marketplace Connect is the easiest and most popular way to keep your product listings and inventory in sync, but it might not be a great fit for your business. If you’ve got a lot of SKUs or you have specific requirements, it might be worth looking into CedCommerce or LitCommerce instead.

Whichever option you end up using, my experience is that once Shopify and Amazon are linked properly, your business runs more smoothly and your day-to-day workflow feels a lot more organized.

Recommended Articles:

• How to Create an Amazon Seller Account (Step-by-Step Guide for 2026)
• How to Start an Amazon FBA Business in 7 Simple Steps (Beginner’s Guide)
• How Much Are Amazon Seller Fees? A Complete Breakdown