Out of the box, Breadcrumbs Uncomplicated and Categories Uncomplicated set your Top-level category to <Root level> (include all menus), which aggregates every menu in your store. We encourage setting it to a specific menu instead - typically Main menu, the Shopify default - so your breadcrumbs follow exactly the navigation you want and nothing else. Renaming, replacing or adding menus in Shopify is when you’ll need to revisit that setting.
How the app picks a top-level category at install
On first install, the app sets the Top-level category to <Root level> (include all menus). That’s a safe starting point - every menu in your store contributes to the trail - but it’s not the recommended long-term setting. If you only have one menu (the Shopify default is Main menu), the trail effectively follows that menu anyway.
This screencast explains the relationship between Shopify menus and the breadcrumb trail - useful background if you’re about to restructure the menus that drive it:
Setting your top-level category
Open Settings in the app (top nav) and pick from the Top-level category dropdown. The recommended choice for most stores is Main menu; for stores with several menus, pick the one that mirrors your category taxonomy, or pick a single menu item to start the trail at a specific branch. Click Save, then click Refresh Categories afterwards so the snapshot rebuilds from the new top-level category.
“I made a new menu called New Main Menu and now nothing works”
A common pattern is to create a parallel menu (titled, say, “New Main Menu”, which Shopify auto-handles as new-main-menu) and point the theme header at it, leaving the original Main menu in place but unused. If the app’s Top-level category is still <Root level> (include all menus), both menus feed the trail, which produces duplicate or overlapping breadcrumbs. The fix is one of two things: delete the stale menu, or set the Top-level category explicitly to the new one.
Multiple menus that drive different things
Your theme’s header navigation is a separate Shopify setting - it points at one menu (usually Main menu). The app’s breadcrumb trail is set independently in Top-level category, so a deep taxonomy menu that you don’t expose in the header can still drive comprehensive breadcrumbs. A fashion store might keep a curated 4-item header menu (Women / Men / Kids / Sale) alongside a 200-item full-taxonomy menu, with Top-level category set to the taxonomy menu so breadcrumbs walk the full tree while the header stays tidy.
A note on collection-only menus
If you have menus whose items are all collection links, breadcrumbs work cleanly. Menus that mix collections, pages, and external links can produce odd trails because the non-collection items don’t slot into the category hierarchy. Keep a dedicated “Categories” menu and set it as the Top-level category if you want to mix link types in your other menus.
Summary
The app follows whichever Top-level category you pick. <Root level> (include all menus) is the initial default, but pointing it at a specific menu (typically Main menu) keeps your breadcrumbs tight and predictable. If your breadcrumbs look wrong after a navigation reshuffle, the Top-level category dropdown in Settings is the first place to check - followed by Refresh Categories.