Human impacts, especially land-use change, are precipitating biodiversity loss. Yet anthropogenic drivers are layered atop natural biogeographic gradients. We ask whether the effects of anthropogenic habitat conversion depend on climatic context. We studied the structure of Anolis lizard communities in intact and human-modified habitats across natural climate gradients in the northern Dominican Republic. Using community-wide mark-resight methods to control for detection bias, we show that the effects of habitat conversion reverse with elevation (and thus macroclimate temperature). Deforestation reduces abundance and biomass in lowland communities but has no such effect at high elevations. In contrast, forest loss results in no compositional change in the lowlands, but complete community turnover between habitats in the highlands. These contrasting community-level patterns emerge from consistent responses of individual species based on their thermal niches. Community reorganization in the highlands stems from thermal niche tracking and habitat switching by abundant lowland species. We find no support for the hypothesis that climate generalists outperform specialists to succeed in anthropogenic habitats. Instead, warm-climate specialists dominate anthropogenic habitats, even in cool macroclimates. Human impacts interact with preexisting environmental gradients to reorganize biodiversity. Leveraging a biogeographic perspective will provide insight into the future communities of life on Earth.