This paper explores the community structure of a network of significant locations in cities as observed from location-based social network data. We present the findings of this analysis at multiple spatial scales. While there is previously observed distinct spatial structure at inter-city level, in a form of catchment areas and functional regions, the exploration of in-city scales provides novel insights. We present the evidence that particular areas in cities stratify into distinct “habitats” of frequently visited locations, featuring both spatially overlapping and disjoint regions. We then quantify this stratification with normalized mutual information which shows different stratification levels for different cities. Our findings have important implications for advancing models of human mobility, studying social exclusion and segregation processes in cities, and are also of interest for geomarketing analysts developing fidelity schemes and promotional programmes.