The Indo-Portuguese Museum, housed in the Bishop's House compound near Fort Kochi, covers the Catholic heritage of the region with a collection of processional crosses, vestments, silver religious objects, and documents spanning four centuries. It's a specialist museum but well-presented, and it illuminates an aspect of Kochi's history — the deep interweaving of Portuguese colonial ambition and Kerala Christian culture — that is easy to miss if you only visit the obvious sights.
The museum is small and takes about 45 minutes. The adjacent cathedral gardens are peaceful and make a good stopping point on a walk through Fort Kochi.