Selling to both everyday retail shoppers and dedicated wholesale accounts is a great problem to have until you’re left with just a handful of units and you’re not sure which channel gets them. This common dilemma of overselling can frustrate both your D2C customers and your B2B partners.
The good news is, you don’t need a second Shopify store or a massive budget to keep your wholesale and retail inventory perfectly separate. Below, we’ll explore four practical strategies to manage wholesale inventory on your Shopify store, so you never have to worry about a wholesale order stealing the last unit from a retail sale again.
Effective Strategies to manage wholesale inventory on your Shopify store
1. Use Multiple Inventory Locations (Shopify’s Built-In Feature)
This is the simplest and most accessible method because it’s built directly into Shopify and doesn’t require any extra apps. It’s the foundation for most other solutions.
How it works: Shopify allows you to track your inventory across different physical or logical locations.
- Create a new location in your Shopify admin called something like “Wholesale Warehouse.”
- Manually assign a portion of your stock for each product to this new location. For example, if you have 100 shirts, you might put 70 in your “Main Warehouse” for retail and 30 in your “Wholesale Warehouse.”
- When a wholesale order comes in, you simply fulfill it from the “Wholesale Warehouse.” Retail orders are automatically fulfilled from your “Main Warehouse.”
The Upside: This method is completely free and works with Shopify’s native fulfillment rules. It gives you a clear visual separation of your stock.
The Downside: This is a very manual process. You have to remember to move stock between locations yourself, and there’s no automatic logic to reserve a certain percentage for wholesale.
2. Duplicate SKUs for Each Channel (The Most Reliable Separation)
This is arguably the most foolproof way to keep your inventory separate because it ensures there’s no overlap whatsoever. It treats your retail and wholesale products as two completely different items.
How it works: You create two versions of the same product. For instance, you might have:
- Retail SKU: HOODIE-RET (public, priced at $40)
- Wholesale SKU: HOODIE-WSH (hidden, priced at $24)
Each version has its own unique SKU and tracks its own inventory. The wholesale SKU is kept hidden from regular shoppers, and only becomes visible to approved B2B partners who are logged in. This can be implemented via a dedicated app called Wholesale Lock Manager B2B.
The Upside: This method offers a perfect, clean separation. You can also use it to create wholesale-specific product variants, like a “case of 12” pack size, that are unique to your B2B channel.
The Downside: It creates more SKUs to manage. Updating product details, like descriptions or images, means you have to do it for both versions.
3. Variant-Level Separation (One Product Page, Two Inventory Pools)
This method offers a nice middle-ground, allowing you to keep your retail and wholesale inventory separate while managing everything from a single product page.
How it works: You create an extra variant on a product, like “Case of 12 – Wholesale.” This variant gets its own inventory count and can be hidden from retail customers.
- You might add a variant option called “Wholesale Only.”
- Then, you use Wholesale Lock Manager B2B to ensure that only approved wholesale buyers can see this specific variant and its inventory count.
The Upside: Your product page, photos, and descriptions are all managed in one place, which is great for SEO and saves you time. Each variant has its own stock pool, preventing any crossover.
The Downside: This method can be a little tricky to set up and may require some custom theme work to ensure the wholesale variants are completely hidden from the public.
4. Using Third-Party Inventory Platforms for Automated Allocation
For businesses with complex operations—multiple warehouses, automated reordering, or international distribution—a dedicated inventory management system might be the best option.
These platforms are designed to sit between Shopify and your fulfillment centers. They can automate rules like “reserve 40% of every incoming shipment for the wholesale channel” or “always keep 50 units reserved for our top distributors.” This keeps your stock perfectly balanced and automatically pushes the correct inventory levels back to Shopify.
Some popular platforms include Skubana/Extensiv, Katana, and Stock&Buy. These are typically for brands that are growing quickly or have very specific multi-location or production-based needs.
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Putting It All Together
For many growing brands, a combination of methods works best. You might use Method 1 (separate locations) with Method 2 (duplicate SKUs) to create a perfect separation of your stock.
Then, you’d add a few key apps to make it all run smoothly:
- Wholesale Pricing Discount B2B: Sets the special prices and volume discounts for your wholesale SKUs.
- Wholesale Lock Manager B2B: Hides those wholesale-only SKUs or variants from public view.
- WSH Order Form & ReOrder: This app lets distributors quickly add dozens of your wholesale SKUs to their cart from a single page, pulling from the wholesale location only.
This trio keeps inventory clean, pricing clear, and ordering painless—all without a second Shopify store or a costly Shopify Plus subscription.
Frequently Asked Questions
What happens if a retail customer tries to buy an item from my wholesale location?
This won’t happen if your setup is correct. When a customer adds an item to their cart, Shopify looks for available stock in all active locations. If there’s no stock in your main retail location, but there is in your wholesale location, the system will still let the retail customer buy it. To prevent this, you must keep the inventory numbers separate using a method like duplicating SKUs or using an app to reserve stock.
Can I automate the process of moving stock between my retail and wholesale locations?
Shopify’s native transfer tool is manual. For automated stock transfers or reservations, you would need to use a third-party inventory app that is designed for “channel allocation.” These apps can be set up to automatically reserve stock for specific channels or transfer it based on a set of rules.
How do these methods affect my accounting and reporting?
Since you’re managing separate SKUs or locations, your reports will show sales and stock levels for each. This is actually a good thing. It gives you a clear picture of how each channel is performing and helps you make better inventory decisions for the future.
Which method is best for a small brand just starting to do wholesale?
For a small brand with a simple catalog, Method 2 (Duplicate SKUs) is often the best choice. It gives you a clear, foolproof separation of stock with minimal complexity. As you grow, you can easily scale up to using separate locations to better manage your fulfillment.
How does multi-location inventory work with fulfillment services like a 3PL?
If you use a 3PL, you would simply add them as a new inventory location in Shopify. You can then assign a portion of your stock to that 3PL for fulfillment. This is a great way to handle regional distribution for your B2B orders or to split your stock between your own warehouse and your fulfillment partner.
What if a wholesale order is a mix of retail and wholesale-only SKUs?
The app-based solutions are designed to handle this. Since the app ties the shipping and pricing rules to the customer’s tag, the checkout process will correctly price and handle all items in the cart according to your wholesale rules, even if they include a mix of items.
Is it possible to set up my inventory so that wholesale customers can see my entire stock, but retail customers can only see what’s in my retail location?
Yes, this is possible. You would set up your inventory to have two locations. Then, you can use a combination of apps to ensure that the retail storefront only displays inventory from your retail location, while the Shopify wholesale app shows a combined inventory count from both locations to your logged-in partners.
What happens if I oversell my wholesale stock?
If your wholesale location or SKU runs out of stock, your wholesale app should prevent further orders from being placed. If an order does go through (due to a manual process or a bug), the order will still be created in Shopify, but you will have to manually source the product or communicate the out-of-stock situation to your partner. This is why keeping your inventory numbers separate and accurate is so important.
