How to Set Up and Manage Shopify Multiple Warehouses [2025]

What happens when your store grows beyond a single warehouse?

Suddenly, it’s not just about keeping products in stock, but deciding which location should ship each order, how to balance inventory across regions, and how to stop stock from sitting idle.

That’s the reality of running Shopify multiple warehouses. It gives you more flexibility and reach, but it also adds complexity that needs to be managed carefully.

We’ll break down how to handle multiple warehouses on Shopify, how to know if you’re ready to add more, the setup and migration process, and the role Prediko plays in keeping everything under control.

Understanding What Shopify “Multiple Warehouses” Means 

In Shopify, multiple warehouses are managed through locations. A location can be a warehouse, a retail store, a third-party logistics provider, or a dropshipper. Each location tracks its own inventory and fulfills orders separately.

When you connect fulfillment apps, such as a 3PL or dropshipping partner, Shopify automatically creates new locations for them. This way, all stock levels across your business are recorded in one system.

Shopify also allows multi managed inventory, meaning a single product can be stored in more than one location at the same time. Orders are then routed according to where inventory is available and where the customer is based.

Having multiple warehouses in Shopify helps reduce delivery times, cut shipping costs, keep stock levels accurate, and give more flexibility in how orders are routed across regions or sales channels.

Do You Need Multiple Warehouses on Shopify? 

Not every store needs more than one warehouse. The decision usually depends on scale, geography, and product mix. 

Adding another location brings benefits, but also adds complexity in stock allocation and coordination. The key is knowing when the benefits outweigh the complexity. 

Here’s how to assess that decision.

Signs It’s Time to Add Another Warehouse 

✅ Order volume: Once daily orders climb above 100–200, single site fulfillment starts to strain

✅ Geographic spread: If a large share of orders ship to regions far from your current warehouse, delivery times and costs rise

✅ Shipping cost delta: Compare what you pay now versus what you would save if you stocked closer to customers

✅ SKU footprint: Larger catalogs and bulky items are harder to manage from one site

✅ Returns complexity: Frequent or regional returns can make a single warehouse inefficient

To make warehouse decisions easier, here’s a simple framework. 

Step 1: Are you shipping more than 100 orders a day?

• No: One warehouse is likely enough.
• Yes: Move to step 2.

Step 2: Are customers spread across distant regions?

• No: A single warehouse is still manageable.
• Yes: Move to step 3.

Step 3: Compare current shipping costs with projected costs if you add another warehouse.

• If savings outweigh the overhead of running a new site: Add another warehouse.
• If not: Stick with one.

Example: A Shopify store selling sports equipment ships 500 orders a day from one East Coast warehouse. Half of its customers are on the West Coast. Shipping from the East costs $12 per order, while West Coast fulfillment would cost $7. 

On 250 daily West Coast orders, that’s a saving of $1,250 a day or over $30,000 a month. The savings more than justify the cost of operating a second warehouse.

Step-by-Step Shopify Multiple Warehouses Setup

Here’s how to set up multiple warehouses from scratch and keep inventory accurate across all locations.

1. Add and name locations

Go to Shopify Admin → Settings → Locations → Add location.

Give each warehouse a clear name (e.g., New York DC or West Coast 3PL) and enter the full address. 

This address is used for shipping rates and tax calculations, so accuracy matters. Once saved, the location appears in your fulfillment list.

2. Configure fulfillment priority

In Settings → Locations, drag and drop your warehouses into the right sequence. The first location with stock available will be used to fulfill the order. Merchants often

• Rank by geography to ship from the closest site
• Rank by cost if one warehouse is cheaper to operate
• Use priority rules for markets, for example, keeping EU orders within Europe

3. Assign inventory to locations

Each product needs to be linked to the right warehouses. Open a product in the admin, scroll to the Inventory section, and select Edit locations. 

Check the boxes for each site that stocks the product, then enter the quantity on hand. Shopify will now track stock separately for each warehouse.

4. Bulk editor and CSV options

If you need to update many SKUs at once, use Shopify’s bulk editor. Go to Products → Inventory, select the variants to edit, and click Bulk edit.

Add columns for each warehouse, type in the correct quantities, and save. 

For even larger catalogs, export your inventory as a CSV. Update the quantities for each location in a spreadsheet, then re-import the file back into Shopify. This method is faster when migrating thousands of SKUs or setting up a new warehouse.

How Shopify Chooses Fulfillment Location 

Shopify looks at three things when deciding where to route an order: the fulfillment priority list you set, whether a single location can fulfill all items, and the routing rules you apply.

1. Fulfillment priority

Locations are arranged in a priority list under Settings → locations. 

Shopify checks this list from top to bottom and assigns the order to the first location that has enough stock to fulfill the item(s). 

2. Minimizing splits

• If one location has all items, Shopify routes the full order there
• If no single location can cover everything, it applies your routing rules
• With “Minimize split fulfillments” enabled, Shopify selects the location that can ship the most items together, even if another warehouse is physically closer

3. When orders get split

Orders split only when no single location has all items. Shopify sends as much as possible from the highest-priority location, then routes the rest to the next available site.

This is where extra shipping cost and slower delivery can appear if stock is spread too thin.

4. Single-location fulfillment

When there is only one location, every order goes there. The only requirement is that the location is active and set to fulfill online orders.

Common pitfalls to avoid include.

• Leaving inactive or “storage-only” sites in the list as they may receive orders by mistake
• Adding a 3PL but forgetting to update the priority sequence as orders route incorrectly
• Counting damaged or reserved stock as “available” as causes unexpected backorders

Regularly reviewing your settings helps prevent split shipments, delays, and misrouted orders.

Advanced Rules and Automation While Using Multiple Warehouses on Shopify

Once multiple warehouses are active in Shopify, rules and automation become important for keeping fulfillment predictable. 

With advanced settings, you can control which warehouse fulfills each order, define exceptions, and manage stockouts without disrupting operations.

1. Allocation rules

You can set rules that decide which warehouse gets the order. Common approaches include ranking locations by priority, choosing the warehouse closest to the customer, or minimizing split fulfillments. 

Rules can also be set by market, so customers in Europe are always served from an EU warehouse.

2. Automation triggers

Automation can determine when orders should be routed to different warehouses. For instance, high-value orders might go to a 3PL with stricter packaging standards, while oversized items are sent to locations equipped to handle them. 

Shopify apps can add even more triggers, such as routing based on order tags, sales channels, or shipping methods.

3. Backorder strategies

If one warehouse runs out of stock, Shopify can route the order to the next location with available inventory. 

Some merchants prefer to allow backorders instead, keeping the order tied to a primary warehouse until replenishment arrives. This avoids split shipments but requires accurate incoming PO data.

Migration Process to Go From a Single Location to Multiple Warehouses 

Scaling from one warehouse to many isn’t just about adding space, it’s also about redesigning how inventory, fulfillment, and data stay in sync. 

Here’s a step-by-step process for making the transition.

1. Audit SKUs

Review your product catalog before adding new warehouses. Remove inactive or duplicate SKUs and clean up bundled products that could cause confusion when stock is split. 

Ensure barcodes and product identifiers are consistent so fulfillment errors don’t appear once multiple locations are active.

2. Freeze sync windows

Pause automated syncs from ERPs, apps, or connected systems during setup. This prevents changes from being overwritten while new locations are created and tested. 

Once all warehouses are live, you can safely re-enable syncs.

3. CSV export

Export your current inventory into a CSV before making changes. This file works as a backup and lets you quickly restore stock counts if an error occurs during setup.

4. Set fulfillment priority

Add your new warehouses in Settings → Locations and arrange them in the correct order. Merchants typically:

• Rank by geography, so orders ship from the closest warehouse
• Rank by cost, so the lowest-cost warehouse is used first
• Rank by market, so international orders stay within the same region

5. Phased migration

Don’t move everything at once. 

Start with a small group of SKUs or a single warehouse. Route only a portion of orders there, monitor performance, then expand gradually. This staged rollout reduces the risk of widespread issues.

6. QA checklist

Before going live, place test orders across locations. 

Verify that stock counts update correctly, orders follow the fulfillment priority you set, shipping rates display as expected, and returns route to the right warehouse. 

Run these checks for both domestic and international orders if you sell globally.

How Prediko Helps Manage Shopify Multiple Warehouses

Prediko is designed to help Shopify merchants manage inventory across multiple warehouses without relying on spreadsheets or manual processes. 

It combines real-time tracking, demand forecasting, and automation to keep stock accurate, orders routed correctly, and replenishment timely. 

Here are the features that make this possible.

• Centralized inventory tracking: View inventory across all Shopify warehouses, 3PLs, and POS locations in a single hub. No more switching tabs or reconciling spreadsheets.

• Real-time sync: Every sale, return, or transfer updates instantly across all locations, reducing errors and avoiding duplicate stock counts.

• AI-demand and supply planning: Prediko’s forecasting drills down to the SKU and location level. By analyzing historical sales data, seasonality, and growth trends, it predicts where, when, and how much stock will be needed. 

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• Automated transfers: Move inventory between warehouses with AI-backed recommendations that balance stock efficiently and cut shipping costs.

• Automated replenishment alerts: Prediko generates alerts when stock falls below thresholds at any of your warehouses. Easily generate and track POs for multiple warehouses, ensuring each site has what it needs, when it needs it.

• Detailed analytics and reports: Prediko offers in-depth analytics and 20+ reports to identify location-specific sales trends, stock movement and health, along with incoming POs, inventory value, and more. You can also schedule reports to your inbox for timely action.

Make Multi-Warehouse Inventory Work for You

Multiple warehouses on Shopify can either improve fulfillment or create inventory chaos. By setting them up correctly, prioritizing locations, and managing stock in real time, you can cut costs, avoid split shipments, and keep customers happy.

Prediko makes it easier with AI-powered forecasting, real-time inventory sync, automated purchase orders, and full visibility across every warehouse. Instead of draining cash flow, your inventory starts driving growth.

Start your 14-day free trial to see how Prediko simplifies multi-warehouse inventory management.

Frequently Asked Questions

How many warehouses can I add to Shopify?

Shopify supports up to 1,000 locations on advanced plans, which can include warehouses, retail stores, or 3PLs.

Will Shopify automatically split my order across warehouses?

Yes. If no single location has all items, Shopify splits the order and allocates line items across locations based on your fulfillment priority.

Do I need a WMS for two warehouses?

Not always. Shopify locations cover the basics, but a tool like Prediko gives real-time visibility and forecasting across both sites.

How do 3PLs show up in Shopify?

When you connect a 3PL, it creates its own location in Shopify so stock levels and fulfillment are tracked automatically.

What are common migration pitfalls?

Unclean SKU data, leaving inactive locations enabled, not freezing syncs during setup, and failing to test fulfillment rules before going live.

How can I prevent split shipments?

Set fulfillment priority carefully and use a system like Prediko to forecast demand and balance stock across warehouses.

Which Shopify apps work best for multi-location inventory?

Prediko is purpose-built for Shopify merchants to manage forecasting, replenishment, and inventory visibility across multiple locations.