How to Do Amazon Shopify Inventory Sync: Step-by-Step Guide

A customer finds your product on Amazon, adds to their cart, and checks out. 

At the same time, another shopper buys the exact same item from your Shopify store. But only one unit was left in stock.

Now you’re forced to cancel the order, issue a refund, and risk a negative review that damages your seller rating. All because your systems weren’t in sync.

If you, like many other multichannel sellers, are tired of dealing with stock mismatches, canceled orders, and unhappy customers, this is for you.

We break down why you need Amazon Shopify inventory sync, the steps to set it up correctly, and the best practices that keep your operations running smoothly.

Why Amazon Shopify Inventory Sync Matters

Selling on both Amazon and Shopify opens up more opportunities, but it also makes stock management more complex. Here’s how: 

1. Overselling risk

Imagine you have three units of a trending product. A burst of Amazon sales wipes out your stock, but Shopify still shows it as available. 

Multiple customers place orders you can’t fulfill, and now you’re facing an avoidable mess.

When stock levels are not updated across platforms in real time, the same product can sell twice before it’s marked as unavailable. This can lead to:

• Order cancellations that frustrate buyers and make them less likely to purchase from you again.
• Refund processing that ties up time and resources, which could be spent fulfilling valid orders.
• Negative reviews that damage your seller ratings and lower your visibility on both platforms.

To avoid this, you need an automated inventory sync so that both platforms update instantly after every sale. 

It ensures you only sell products that are actually in stock, protecting your reputation and keeping customers happy.

2. Customer dissatisfaction 

Unsynced inventory across channels can turn an eager buyer into a lost customer. They place an order expecting quick delivery, only to find out days later that the product is not available.

Research from PwC shows that 32% of customers stop doing business with a brand they love after just one such bad experience.

Real-time, centralized inventory visibility allows customers to only purchase what is available. This helps you deliver on expectations, maintain positive ratings, and encourage repeat business.

3. Operational delays

Inventory errors do not just cause lost sales. They slow down everything behind the scenes. 

Teams end up pausing fulfillment to sort through incorrect orders, verify stock, and contact customers about changes. Every extra step adds hours or even days to delivery timelines.

During busy periods like promotions or Black Friday, these delays can pile up quickly. 

A single stock mismatch can disrupt multiple orders and push shipping back for dozens of customers.

4. Efficiency gains from fewer manual updates

Every order that comes in on Shopify or Amazon needs an inventory adjustment. Without automation, that means logging into both platforms and updating stock by hand, over and over again. 

It’s slow, repetitive work, and even a single missed change can create a mismatch that leads to bigger problems later.

With real-time sync, stock updates happen automatically the moment a sale is made. Your team no longer spends hours chasing numbers, and you reduce the risk of human error entirely. 

The time saved can be used for marketing, launching new products, or improving customer service.

Methods for Amazon Shopify Inventory Sync: Official Integrations and Beyond

Shopify offers official integrations and apps that connect directly with Amazon, covering everything from product listings to fulfillment management. Here are the key ones.

1. Marketplace connect

Marketplace Connect links your Shopify catalog to Amazon, allowing you to manage listings and pricing from one place. It provides a two-way sync of inventory and orders.

When a sale happens on Amazon, the product count is updated in Shopify automatically, and orders placed on Amazon appear in your Shopify admin for processing.

2. Amazon MCF app

Next is Amazon Multi-Channel Fulfillment (MCF) that connects Shopify orders directly to Amazon’s logistics network. 

With this integration, your inventory is stored in Amazon’s fulfillment centers, and when an order is placed on Shopify, it is automatically sent to Amazon for picking, packing, and shipping.

3. CED Commerce

CED Commerce is an integration app that connects Shopify with Amazon while giving merchants more flexibility than Shopify’s native integrations.

Beyond syncing inventory and orders, it supports bulk product uploads, advanced pricing rules, and multi-account management. 

For brands selling on multiple Amazon marketplaces (like US, UK, or Canada), the app helps centralize operations inside Shopify, making it easier to stay in sync and scale globally.

Third‑Party Amazon Shopify Inventory Sync Tools

Syncing inventory across Amazon and Shopify requires more than just built-in integrations. 

Many merchants rely on third-party tools to handle complex workflows, such as managing large catalogs, syncing across multiple warehouses, or reconciling high order volumes during sales spikes. 

These apps go beyond the basics by offering features like

• Real-time sync across multiple marketplaces and sales channels
• Advanced channel-wise inventory forecasting to predict demand and prevent stockouts
• Bulk listing and catalog management for larger product ranges
• Multi-warehouse support to allocate inventory across different fulfillment centers
• Granular analytics and reporting for smarter decision-making

See a complete breakdown of all the available Shopify sync apps.

How Prediko supports Amazon Shopify inventory sync

If you want a tool that not only syncs inventory but also helps you plan and manage stock across both platforms, Prediko should be your choice.

To make Prediko work with Amazon (and other marketplaces), you’ll first need to route those orders into Shopify using an app like CED Commerce. 

This centralizes your Amazon demand in Shopify, allowing Prediko to capture your full multichannel sales data. Once that’s in place, here’s how Prediko supports you.

• Real-time multi-location inventory tracking: Prediko continuously monitors inventory across Shopify and Amazon, updating quantities automatically whenever a sale is made. Even if you store stock across multiple warehouses or fulfillment centers, Prediko keeps both platforms aligned so product availability is always accurate.

• AI demand planning: Selling on both Amazon and Shopify can make forecasting demand tricky. Prediko analyzes your historical data, seasonality, and sales patterns across both platforms to predict how much stock you’ll need. 

• AI supply planning: When Amazon and Shopify orders come in at the same time, Prediko creates smart buying plans that combine demand from both channels. It tells you what to order, when to order, and in what quantities, keeping your supply chain balanced.

• Purchase order management: Prediko makes replenishment easier by automating purchase orders linked directly to your Amazon and Shopify demand. Create, update, and track POs automatically, including supplier lead times and delivery schedules. 

• Analytics and reports: Prediko provides 20+ report templates designed for multichannel sellers. You can track Amazon and Shopify sales trends, monitor inventory turnover, and set low-stock alerts. This visibility helps you spot sync issues quickly and make decisions before they impact your customers.

Step‑by‑Step Setup for Amazon Shopify Inventory Sync

To set up inventory sync, you’ll need to meet a few key requirements and follow the steps below to ensure the process runs smoothly and error-free

1. Set up your Amazon Pro Seller account

To sync inventory between Shopify and Amazon, you must have an Amazon Professional Seller account. The Individual Seller plan does not allow access to the necessary APIs that make real-time updates possible. 

If you already have an Individual account, log in to Amazon Seller Central and upgrade to the Professional plan. This requires a monthly subscription fee but gives you the technical permissions needed for integration.

Once your Professional account is active

• See if your business information, bank details, and tax information are fully verified in Seller Central
• Check that your products comply with Amazon’s listing requirements, including UPC/EAN/ISBN identifiers
• Ensure you have access to the Marketplace Web Service (MWS) APIs or the newer Selling Partner API (SP-API), since these are what sync apps use to exchange data between Amazon and Shopify.

Completing this step makes your Amazon account eligible for integration so that inventory updates can flow through without disruptions.

2. Clean up product data in Shopify 

Before connecting Shopify to Amazon, your product data needs to be standardized. The sync relies on identifiers like SKUs, variants, and barcodes to match products between platforms.

If these are inconsistent, the integration will fail or create duplicate listings.

Key actions to take

• Verify SKU naming: Every product and variant in Shopify must have a unique SKU. Use the same SKU in Amazon so the system can map inventory correctly. Even small differences (extra characters, dashes, or spaces) will break the sync.
  
  For example, if a SKU in Shopify is “TSHIRT-BLK-M” but on Amazon it is “TSHIRT-BLK-M-01,” the two will be treated as separate products.
  
  
• Check variants: Make sure all size, color, or style variants are set up properly in Shopify. Each variant should have its own SKU and barcode.
  
  
• Add valid barcodes: Assign UPC, EAN, or ISBN codes where required. Amazon uses these to validate listings, and many sync apps need them to connect products.

Cleaning up product data at this stage prevents mismatched inventory counts later. A short audit now saves hours of fixing errors after the sync is live.

3. Install and configure the sync app or integration

Once your product data is cleaned up, the next step is to set up the integration between Shopify and Amazon. Shopify’s official options are Marketplace Connect and the Amazon MCF app, but you can also use third-party apps like CED Commerce if they better fit your workflow.

To install

1. Go to Shopify App Store and search for the app you want to use (e.g., “CED Commerce”, “Marketplace Connect”, or “Amazon MCF”)
2. Click Add app and follow the prompts to install it in your Shopify admin
3. Connect your Amazon Professional Seller account by logging in when prompted and granting the required API permissions

After installation, configure the app:

• Map your SKUs so the system knows which Shopify products correspond to which Amazon listings
• Set pricing and listing rules if you want Amazon prices to match or differ from Shopify
• Enable order sync so sales on Amazon flow into Shopify for centralized fulfillment tracking

Proper configuration ensures the two platforms exchange accurate product, price, and order data without duplication or mismatches.

4. Enable inventory tracking and sync rules

Inventory tracking must be turned on in Shopify for every product you plan to sync. Without tracking turned on, Shopify cannot monitor stock levels or send updates when items are sold.

Next, configure sync rules inside your app. Decide how frequently inventory should be updated, whether prices will be synced, and how orders from Amazon should appear in Shopify. Setting these rules clearly avoids surprises later. 

5. Add buffer stock logic to reduce overselling

Even with real-time syncing, delays of a few minutes can cause overselling during peak traffic. To protect against this, set up a buffer stock.

This means reserving a small portion of inventory (e.g., 2–5 units) that will not be published to either channel. 

For example, if you have 50 units, you might only list 47 as available. Most integration apps include buffer stock settings you can enable.

This small safeguard gives you room to handle sync delays, cancellations, or last-minute adjustments without letting customers order products you can’t ship.

6. Test sync with manual changes and order simulations

Before going live, test your sync thoroughly. Start by adjusting stock levels in Shopify and confirm that the changes appear correctly in Amazon.

Then do the same in reverse. Next, place test orders from both platforms and verify that inventory updates accurately and orders flow into Shopify without errors. 

Check fulfillment workflows so that Amazon or your chosen method processes them correctly.

Testing helps catch SKU mismatches, sync delays, or incorrect rules before they affect real customers. A short testing phase builds confidence in the system once it’s live.

How to Avoid Shopify Amazon Inventory Sync Problems in 2025?

By now, you’ve learned how to set up Shopify Amazon inventory sync. Once the system is running, it’s important to follow a few best practices to prevent any disruptions. 

1. Always enable "Track quantity" for products

Inventory sync will not work if “Track quantity” is turned off in Shopify. Without it, stock levels cannot be monitored or updated automatically, which means sales on Amazon will not reduce counts in Shopify. 

Go into each product’s settings and confirm that “Track quantity” is selected for all synced products. It’s a small step, but forgetting it is one of the most common causes of sync failures. 

Making it part of your product setup routine ensures that every new listing is always connected to real-time inventory updates.

2. Maintain buffer stock and monitor sync logs

Even with automated syncing, there can be slight delays during high traffic periods. To protect against overselling, maintain a small buffer stock.

This means holding back a few units from being listed so you can handle last-minute orders or sync lags. 

Most apps allow you to set buffer stock rules. 

In addition, make a habit of checking sync logs in your app’s dashboard. Logs show when updates are pushed and flag any failed attempts.

Regular monitoring helps you catch problems before they reach customers, giving you time to fix errors without impacting orders.

3. Audit SKUs regularly for mismatches

SKU mismatches are one of the most common reasons inventory sync breaks down. A small difference, such as an added dash, space, or character, can cause Shopify and Amazon to treat two listings as separate products. 

To prevent this, schedule regular SKU audits. At least once a month, compare your product catalog in Shopify with your Amazon listings and look for discrepancies. 

Correcting these early avoids bigger issues like duplicate listings or untracked stock. A simple, ongoing SKU audit process keeps your data consistent, and your sync continues working as expected.

4. Check sync latency and accuracy periodically

Different apps push updates at different speeds, and performance can vary depending on sales volume. To avoid surprises, test your system regularly.

Make a small stock adjustment in Shopify and track how long it takes to appear in Amazon, and then do the reverse. 

Periodic checks confirm that your sync is not only working but also updating quickly enough to meet customer demand. 

If latency is too high, you may need to adjust your app’s settings or switch providers. Monitoring accuracy and speed gives you confidence that your inventory is always aligned.

Start Multichannel Selling with Amazon Shopify Inventory Sync

Keeping your Shopify and Amazon inventory in sync is crucial for preventing overselling, reducing customer frustration, and eliminating manual fixes. This way, you can maintain accurate stock counts, faster fulfillment, and smoother operations.

This guide walks through everything you need to know about Amazon Shopify Inventory Sync, from account setup and product data cleanup to installing integrations, enabling sync rules, and testing your system.

With the right process and tools in place, inventory sync becomes the backbone of multichannel growth.

Prediko helps Shopify brands gain complete control and visibility over multi-channel inventory, so you spend less time troubleshooting and more time scaling your business.

Start your 14-day free trial and see how Prediko can help you with multi-channel inventory management.

FAQs

How can I sync my Shopify inventory with Amazon in real-time?

You can use Prediko, CED Commerce, Shopify’s Marketplace Connect, or Amazon MCF to update stock automatically across both platforms.

What are the best tools or apps for Amazon and Shopify inventory synchronization?

Prediko is built for Shopify sellers who want unified control over their inventory. Other options include CED Commerce, Marketplace Connect, Amazon MCF, and other third-party apps. 

How does syncing inventory between Shopify and Amazon prevent stockouts or overselling?

Real-time sync updates inventory the moment an order is placed, ensuring items are instantly marked as unavailable on other channels so customers never purchase products that are already sold out.

Is it possible to automate inventory updates between Shopify and Amazon?

Yes. Prediko and other integrations automatically push inventory updates between Shopify and Amazon, removing the need for manual adjustments.

What are the steps to set up inventory sync between Shopify and Amazon?

Set up an Amazon Pro Seller account, clean up SKUs and barcodes in Shopify, install a sync app like Prediko, enable tracking, add buffer stock, and test.