Context <p>Changes in landscapes due to the conversion of natural vegetation into agroecosystems are causing an alarming and rapid loss of biodiversity on a global scale.</p> Objectives <p>We assess how local environmental factors and landscape structure influence Squamata reptiles’ abundance, and alpha and beta diversities in agricultural landscapes in the Brazilian Cerrado.</p> Methods <p>We sampled 20 sites using active visual search and pitfall traps to record Squamata reptiles’ abundance and richness. For each sampling site, we measured seven variables of vegetation structure at local scale and calculated four landscape metrics at five spatial scales.</p> Results <p>We recorded 145 individuals of 30 Squamata species comprising 15 lizards, 12 snakes, and three amphisbaenians. Agriculture cover had a negative effect on lizards’ abundance and richness. No effect was found on the abundance and richness of snakes. Species turnover was the major process responsible for Squamata reptile dissimilarity among sites. Reptile total beta diversity and species turnover were influenced by variations in the number of trees at the local scale.</p> Conclusions <p>Our results highlight the negative effects of agriculture expansion on species abundance and richness in lizard communities. Moreover, vegetation structure may act as an environmental filter and predict the variation in Squamata reptiles’ species turnover between sites. Our findings show that maintaining well-preserved patches of natural vegetation in agricultural landscapes is of utmost importance for Squamata reptiles’ conservation and should be considered in landscape conservation and management design.</p>