Once a Shopify catalog reaches a certain size, the hard part is no longer adding products, it is keeping the whole thing understandable for customers and for your own team. Collections, filters and navigation all grow together, and small decisions early on can make the store feel either straightforward or heavy a year later.
What I see quite a bit is a catalog that started very clean. Over time, new ranges, brands and campaigns get their own collections and menu items. None of those decisions are wrong on their own, but eventually you end up with overlap and it becomes harder to explain to a new team member how everything fits together.
The way I usually approach this on Shopify is:
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Define a small “spine” of permanent collections – your main product types, key brands, and evergreen sets like new arrivals and sale. Those get stable URLs and a fixed place in navigation.
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Be clear on collection vs filter – if you plan to send traffic to a set of products repeatedly from menus, email or ads, it usually deserves a collection. Otherwise, push it into filters powered by product type, tags or metafields.
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Default to automatic collections where the logic is stable – use product type, vendor and tags so new products fall into the right places without manual work. Keep manual collections for curated campaigns and stories.
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Work on new navigation in an unpublished theme – collections are store-level, but menus and templates live per theme. I test new menus and layouts in an unpublished theme until common journeys feel natural, then roll them out.
For very large catalogs, doing this only inside the admin can get slow. In those cases I find it easier to work with collections in bulk via CSV. I help my merchants with a tool called Collections Import Export Pro that does this, but the approach above still works even if you build and edit everything directly in Shopify.
I would be genuinely interested to hear what rules other merchants and partners use to keep large catalogs organized so the store still feels simple to shop.