Rocky environments host rich levels of biodiversity and provide vital habitat for specialised organisms, range-restricted species and a broad range of ectotherms adapted to saxicoline environments. In Australia, rock habitat is being destroyed during soil amelioration practices associated with agricultural intensification. Advances in rock crushing technology, developed to expand or increase crop yields and efficiency, pose an undocumented threat to global biodiversity, especially reptiles dependent on non-renewable rock habitat in agricultural landscapes. Rock removal is a legislated key threatening process in parts of Australia and will accelerate biodiversity loss if not mitigated. We estimated reptile species’ range overlap with dryland cropping and modified pastoral regions within the Australian wheat-sheep zone to assess the potential impacts of rock crushing practices. We examined species- and family-richness within the impact zone and across bioregions within the impact zone, to identify areas where rock removal has the greatest potential to impact terrestrial and fossorial squamates. Our analysis revealed that 159 potentially impacted reptile species occur within the study area, representing 16% of Australian terrestrial squamates. Fourteen of these species, including six threatened species, have more than 50% range overlap with areas of intensive agriculture, and include several endangered pygopodids, scincids and agamids. Bioregions rich in rock and burrow-dwelling reptiles include the Brigalow Belt South, Murray Darling Depression, Darling Riverine Plains, Eyre Yorke Block, Avon Wheatbelt, Nandewar, Flinders Lofty Block and New South Wales South Western Slopes. Synthesis and applications. The conservation of reptiles in agricultural landscapes requires appropriate management and retention of surface rocks. Potential yield increases from destroying rock habitat to intensify or expand cropland will not compensate for the net loss of reptile populations dependent on non-renewable resources. Financial incentives to prevent the expansion and transformation of non-arable landscapes to cropland are required to prevent the ongoing loss of biodiversity.