Abstract Species distributions and the mechanisms that produce patterns in the occupation space are recurrent themes in community ecology. Here, we examine beta diversity among assemblages of small mammals in the Cerrado domain of Brazil to partition the effects of turnover and nestedness on species distributions. Our objective was to evaluate whether balanced spatial variation in abundance (β bal) and abundance gradients (β gra) are congruent within and among habitats and localities of the Brazilian Cerrado. In addition, we wanted to understand whether ecological mechanisms, such as dispersal limitation, habitat filtering, and species sorting, drive the distribution patterns of the Cerrado small mammals. We analyzed the occurrence and abundances of small mammals from 16 localities widely distributed across the Cerrado biome, and grouped our data with respect to two distinct spatial scales. Baselga’s Bray–Curtis index of dissimilarity and its respective partitions, i.e., balanced variation in abundance (β bal) and abundance gradients (β gra), were estimated between sampling units at the two spatial scales. Thus, we used exponential models to search for distance decay in species similarity between pairs of localities and between similar habitats. Our results show that differences between small mammal assemblages in the Cerrado are driven mainly by species replacement rather than independent gain or loss of species, both at small and large scales. The spatial turnover patterns of small mammals in the Cerrado biome are determined by a combination of large scale (biogeographic, spatial) and local mechanisms (low dispersal and habitat specificity). However, processes occurring at small scales seem to be more important in species sorting than processes occurring at large scales. The spatial configuration of the landscape and the extent and quality of habitats strongly influence the rate of species turnover in Cerrado. Thus, protecting the different types of habitats should be of prime importance to conserving the diversity of Cerrado small mammals.