Microrefugia play a key role in facilitating the persistence of biodiversity during climate change. Many occur in topographically complex landscapes shaped by various disturbances, but we know little about how the combined effects of topography and disturbance affect the capacity of refugia to support biodiversity. To better understand this, we inventoried taxonomic richness across four biological groups (soil microbiota, vascular plants, terrestrial snails, and ants), as well as climatic and soil conditions, in different microhabitats (south-facing slopes, north-facing slopes, and bottoms) of topographic depressions (dolines) and on the surrounding plateaus. Unique species assemblages and cooler, moister microclimatic conditions in dolines supported their importance as biodiversity hotspots and microrefugia. Relationships between indicators of disturbances (anthropogenic: historical logging; natural: canopy gaps) and species richness differed, depending on the biological group and microhabitat. While most biological groups seemingly recovered within 50 years following clear-felling, plants did not, highlighting the persistent impact of anthropogenic disturbances on refugial capacity. Plants were also the only group that displayed a significant response to the presence of small canopy gaps at doline bottoms, which promoted the occurrence of specific plant species. All biological groups displayed some response to microhabitats, although these responses differed among taxa. Therefore, high environmental heterogeneity appears to help facilitate the role of dolines as biodiversity hotspots and microrefugia. We conclude that the direction and magnitude of the effects of disturbances and topography are taxon-specific, due to species-specific responses to microenvironmental conditions. Disturbance history is an important consideration when identifying refugia for climate change management.