How to Sync Inventory Between Two Shopify Stores – Manual vs. Automated

Expanding to a second Shopify store opens new growth opportunities until inventory discrepancies start cutting into sales and damaging customer trust.

Here’s what happens when your Shopify stores aren’t synced:

• Store A sells out but Store B still shows stock, leading to canceled orders and customer frustration. 
• You add a new product to Store A but forget to update Store B, leaving money on the table.
• A pricing update in one store doesn’t sync with the other, confusing customers and hurting trust.

To keep your stocks accurate across both stores, you need to sync inventory between two Shopify stores. There are two options: manual syncing (tedious and error-prone but doable) or automated Shopify inventory sync using a tool like Webgility.

How to manually sync inventory between two Shopify stores

If you’re set on manually updating stock, here’s how you can do it.

1. Sign in 

Log in to both of your Shopify stores separately. Ensure you have access to the admin dashboards of both the stores. 

2. Select a theme for both stores 

Go to Online Store > Themes in both stores. 

Ensure both stores use the same (or compatible) themes so that imported product data displays correctly.

3. Export CSV files

• Navigate to Products > All Products in store A. 
• Click ‘Export’ and choose CSV for Excel, numbers, or other spreadsheet programs.
• Select ‘All Products’ (or a specific collection to sync specific SKUs).
• Click ‘Export Products’ and download the file.

4. Prepare product media for import 

First, export the CSV file from Store A. Then, before importing it into Shopify, ensure all product images are hosted online. Shopify's import system requires each product to have a valid image URL, so double-check that every image link works.

If the URLs are missing, you can upload images to Shopify’s file library (Settings > Files) and link them in the CSV. 

Also, review product names, SKUs, and inventory counts to avoid mismatched or duplicate listings.

Here’s how to review product names: 

• Open your CSV file in a spreadsheet tool (Excel or Google Sheets).
• Check for duplicate SKUs — each SKU should be unique.
• Verify inventory counts match what’s available in Store A.
• Ensure product names are consistent to prevent confusion.

5. Import CSV files 

To bring the products into Store B, head over to Products > Import, click Add file, and select the CSV you just prepared. 

Shopify will generate a preview. Double-check that everything looks accurate before proceeding, then upload to continue. Depending on the number of products, this can take a few minutes to an hour. 

Your CSV file holds the latest inventory data, allowing you to calculate stock levels and keep product pages updated.

But can manual syncing keep up as your ecommerce business scales?

Pro tip: Set calendar reminders to export and import CSVs regularly, otherwise, inventory mismatches will sneak up on you.

Why manual syncing fails as you scale 

If you're managing fewer than 20–30 products, handling inventory updates manually might still be manageable. However, as your catalog grows beyond 50 products, you need to automate inventory management to track stock levels accurately. 

• Massive time sink in adjusting tax rates manually: If you're selling globally, you have to adjust tax rates and currency settings manually for each store. (that's extra time spent tweaking settings than selling) And the more locations you sell to, the more time-consuming this becomes.
• Product media doesn't transfer automatically: When you export a CSV, it only moves text-based product details. To export images and videos, you'll have to upload them manually for every product. Even if you have 50 products, this step alone may take up hours of extra work. Imagine doing this for every pricing change or new collection launch. 
• Prices and discounts need manual updates: As a multi-store owner, you'd run region-specific promotions. Now, without an automated Shopify inventory sync in place, you will need to adjust pricing for each store manually. If you forget to update it to another store, customers may see inconsistent prices, leading to abandoned carts. 
• No real-time inventory sync: Even if updating inventory in one store takes up half an hour, doing the same for two doubles the effort. Add regular updates, and manage errors, and you lose hours each week only on syncing. 

There’s a smarter way. 

Automate Shopify inventory sync and save hours with Webgility  

Automated multi-channel Inventory management helps ecommerce businesses scale faster as you can sync stock levels in real-time, automate tax settings, and bulk update product listings. 

For instance, Rider Shack, a surf shop based in Los Angeles, faced significant challenges in managing over 13,000 products across their retail and online stores. The manual process of entering online sales into QuickBooks and syncing inventory was labor-intensive and led to frequent errors, including out-of-stock issues that resulted in canceled orders and dissatisfied customers.

After implementing Webgility, they reduced inventory management tasks by 15 hours per week, and the operational costs decreased by $1,400 monthly due to increased efficiency. Here’s how: 

• Real-time inventory syncing: Webgility connects all your Shopify stores to a single dashboard, so stock updates happen automatically across every store.

The moment a product sells in Store A, Webgility updates the inventory count in Store B (and vice versa), preventing stockouts, overselling, and manual reconciliation. 

• Automated tax calculation across the stores:  If you're selling internationally or in different states, tax rates can vary between stores. Webgility ensures each store applies the correct tax settings automatically, keeping pricing and reports accurate while reducing manual adjustments. This helps you avoid tax miscalculations that could lead to compliance issues or revenue discrepancies.

• Bulk product updates without CSV import-export: You can adjust stock levels, pricing, and product descriptions across multiple stores instantly, without the hassle of exporting and importing CSV files. Whether you need to adjust stock levels, pricing, and product descriptions across all stores, you can do so without CSV import/export required.

Sync inventory with Webgility in 5 easy steps 

Before we begin, verify that at least two of your sales channels are connected and configured in Webgility Online. If you sell on Amazon and eBay, ensure both accounts are linked to Webgility. 

When more than one sales channel is connected, you will see the Multi-channel Inventory Sync option in Webgility Online. Then, follow these steps. 

1. Go to Products > Multichannel Sync

2. Choose the master inventory

Select the store or system that will act as the source of truth for inventory levels. This is where all stock updates will originate.

3. Choose your non-master inventory

Identify the stores that will receive inventory updates from the master inventory. These stores will automatically sync based on the master store’s data.

4. Choose the matching criteria 

Decide how products will be identified across stores. This could be by SKU, barcode, or product title. Choosing the right criteria ensures accurate matching. 

5. Click on Save

Once everything is set up, hit Save to apply the settings. From here, inventory will sync automatically, keeping stock levels accurate across all stores.

Once complete, all of the items you have mapped will have their quantities synced on an hourly basis with the master inventory sales channel. You may repeat the same steps to sync the quantities with your other sales channels.

You can watch the demo of this feature here. 

Every hour you spend manually updating inventory is an hour you could be selling. 

With Webgility, your stock updates itself so you never oversell, run out of stock, or waste time on spreadsheets. Streamline your inventory across multiple stores with Webgility. 

Get started for free today to see it in action!