Landscape modification is a key driver of global species extinction. Thus, understanding how species react to changes is essential for effective conservation management in modified landscapes. We examined the impact of selected land use patterns on the critically endangered Ceratophora tennentii in the Knuckles mountain range of Sri Lanka where lizards occupy patches of both natural undisturbed forests and modified plantations – evidently, those with a forest canopy. We tested three potential explanations for non-random habitat selection: availability of suitable microhabitat pockets, availability of prey and direct threats from humans. The microhabitat pockets occupied by the lizards were characterised by shade, humidity and the density of perches. Most lizards were found in mixed cardamom forests followed by natural forests and cardamom plantations, but none were observed in the pine plantations. Food availability showed similar patterns among habitats. Direct mortality by humans did not influence the distribution of this species. Our work indicates that habitat modifications that retain the structural complexity of the vegetation would still permit the existence of the species in densities equal to or greater than that of undisturbed forest patches. It adds to a growing body of literature that signifies the importance of disturbed habitats (intermediate disturbance hypothesis) in protecting threatened species of fauna. It is highly unlikely that some disturbed habitats will be ever be returned to their former pristine state in time frames that are important for species’ conservation. Hence, attention is needed in developing suitable approaches to manage and conserve species across disturbed habitats.