Khawa Karpo, in the eastern Himalayas, is a mountain considered sacred throughout Tibet, and is internationally recognized as a global biodiversity hotspot. Numerous areas within this landscape are considered ‘sacred’ by the indigenous Tibetans of the region, who interact with these sites in ways potentially beneficial to conservation. Our previous remote sensing study indicated that sacred sites are found in habitats with greater species richness, diversity, and endemism than randomly selected non-sacred sites. This study examines the role of sanctity in biodiversity conservation within habitats in the Khawa Karpo region by pairing plots within the same habitats in sacred and non-sacred areas. Understory richness, diversity, cover, and number of useful species are measured; for trees, richness, diversity, cover, and density are measured. Results indicate that within habitats sanctity does not affect understory plant communities; however, within sacred areas trees are larger (p = 0.003) and forests have greater cover (p = 0.003) than non-sacred areas. Our results indicate that, whereas placement of sacred areas and preservation of vegetation cover affects useful plants, biodiversity and endemism, within habitats sacred sites preserve old growth trees and forest structure. In sum, Tibetan sacred sites are ecologically unique and important for conservation on varying scales of landscape, community, and species.