We have recently taken over a similar business in a different location that is already established. What we want to do is pretty much have both domains work from the same backend of shopify whilst keeping the websites and brands distinct.
There will be slight stock overlap but a variance between the two store.
What I was currently thinking is that we can utilise our main store with locations for POS for both stores, and then have a separate Shopify store for the established brand which will pretty much be online only, we would then use a store sync app for any overlapped stock.
Is there an easier way to do this that keeps everything together? We want to keep the new stores established brand power whilst taking everything under one hood pretty much.
Actually, there’s no native way to fully manage two distinct storefronts under one Shopify backend.
Maybe your best option is “Shopify Plus with Shopify Markets”, it means if your businesses serve different regions, you can manage both brands under one store with unique domains, pricing, and branding per market.
And, because you want to keep the brand identities distinct, running two stores with an app like Matrixify, Syncio, or Stock Sync can help sync inventory and orders where needed.
Since you want to keep both brands and websites distinct while still bringing operations under one roof, finding a solution that can handle inventory and product data for only the overlapping products is probably the key here.
I recommend checking out Easify Inventory Sync. It can handle this type of setup using a Source Store and Destination Store approach:
The Setup: Your main store can act as the Source Store, while the established brand operates as a separate Shopify store connected as a Destination Store.
Selective Sync: Since you mentioned there will only be partial stock overlap, you can choose exactly which products should be synchronized between stores. Shared products stay aligned automatically, while unique products remain completely independent for each brand.
Inventory & Product Data Sync: In addition to inventory levels, the app can also sync product information such as descriptions, images, pricing, and other product details. This helps reduce duplicate work and keeps shared products consistent across both storefronts.
This approach lets you preserve the existing brand identity, domain, and customer experience of the acquired business while still centralizing the management of overlapping products.
Easify is definitely worth adding to your shortlist if you’re exploring multi-store inventory solutions. If you have questions about whether your setup would work well with a Source Store / Destination Store structure, the Easify team is always happy to help
Your two-store plan is probably the right starting point. I would not choose the sync app until you have written an ownership matrix for the overlapping products.
For each shared SKU, decide separately:
Inventory: which store or external system is the single source of truth? Prefer one-way sync unless you have a clear conflict rule.
Product content and price: sync only the fields that are intentionally identical. A shared SKU does not necessarily mean shared titles, pricing, images, or metafields.
Store-specific data: keep unique products, metafield definitions, theme references, customer records, and app configuration independent. IDs from one store should never be assumed to work in the other.
Before rolling it out, test 5–10 overlapping SKUs and simulate a sale in each store, refund/restock, SKU rename, temporary sync outage, and a product edit on both sides. Ask the vendor what happens after an outage and which value wins when both stores changed the same field.
That gives you central control where it helps without accidentally flattening the differences that preserve the acquired brand. If this acquisition setup is still current: are you also repeating product, variant, metafield, or theme changes across both stores, or is shared inventory the only cross-store operation? That distinction determines whether you need a focused inventory sync or a broader multi-store operating workflow.
If you want to keep both brands on separate Shopify stores with separate domains while automatically syncing inventory for overlapping products, Inventory Sync – GoGo might be worth checking out.
It syncs inventory for duplicate products in real time based on the same SKU, so whenever inventory changes in one store, it is automatically updated in the other. This allows you to keep both brands completely independent without having to manage inventory manually.
This is a setup that many merchants use when managing multiple Shopify stores that share the same physical inventory.
