We assessed the variation of both composition and functional diversity of mammals along an elevation gradient (1600–3600 masl) at the Tabaconas Namballe National Sanctuary (TNNS) in northern Peru. Using a camera-trap design (85 stations, 8,825 camera days, ~ 317 km2), we recorded a total of 33 mammalian species during the dry season of 2016. Species-specific effects of environmental covariates based on multi-species occupancy modeling showed that only elevation had a statistically significant effect on occupancy. Also, a principal coordinate analysis and a distance-based redundancy analysis suggested that the variation in species composition is mainly explained by elevation, and moderately by both the normalized difference vegetation index (NDVI) and the distance to roads. The highlands appear to be dominated by a reduced assembly of species consisting of the montane guinea pig, the Andean fox, and the northern pudu. Functional diversity decreased with elevation, providing evidence that lowland and highland communities are functionally dissimilar. Moreover, land-use is changing rapidly in the areas surrounding the TNNS, suggesting that increased connectivity at the two extremes of the elevational gradient (the highlands and the lowlands) will ensure the long-term viability of terrestrial mammalian populations and, thus, the ecological processes in which they are involved.