Habitat loss and fragmentation are leading threats to biodiversity and have been implicated in population declines worldwide. In agricultural landscapes where natural habitat has been extensively modified, remnant patches can preserve species richness and diversity. However, the persistence of some organisms is dependent on a species' ability to move between habitat patches. The effects of habitat loss and fragmentation on reptiles in semi-arid agricultural landscapes, and the relative impact of cropping and grazing, are poorly described. We aimed to investigate the effect of habitat fragmentation on semi-arid reptiles by comparing species richness and diversity between continuous habitat and patches embedded within different land use types (cropping and grazing). Reptiles were surveyed using pitfall traps, funnel traps and active searches across 20 sites stratified by site, vegetation and land use type. Twelve sites were established in remnant mallee woodland patches embedded within an agricultural matrix, and eight sites were established in a private conservation reserve on the same property. Generalised linear models were used to explore relationships between reptile species richness and diversity and design variables. A total of 480 individuals from 31 species were recorded. Reptile species richness was significantly higher in the reserve compared to patches. However, these differences were driven more by reductions in species richness in patches embedded within a grazing matrix, which had fewer species than patches embedded within a cropping matrix. Sites within sand plain vegetation had higher diversity than sites within dune mallee vegetation. Our findings suggest semi-arid reptile species are sensitive to habitat loss and fragmentation associated with land clearing. Therefore, protecting large areas of intact habitat on private property is required to maintain reptile diversity in semi-arid landscapes subject to land use change. Managing patches of remnant vegetation within the agricultural matrix through grazing exclusion may also serve to retain reptile diversity.