Fire is a global disturbance that has a strong influence on biodiversity. Seasonal fires are common in neotropical savannas of South America, yet few studies have analyzed how the fauna of these habitats and nearby forests respond to fire. We evaluated the effects of fire on the community of non-volant small mammals in the Colombian llanos by comparing their populations in both unburned (no record of fire for the last 20 years) and recently burned areas (three years after the last fire event). Vegetation structure was monitored at 240 plots. We used hierarchical single-season occupancy modeling to determine potential effects of fire on small mammal detection and occupancy. Our results indicate that fire has long-term effects on plant diversity and richness, as well as on the species composition. Three years after the last fire event, the average richness of plant species at burned sites was lower than at unburned sites. Fire also affected the distribution of vegetation strata leading to an increased abundance and diversity of plants in the ground and herbaceous strata in burned plots. The hierarchical models indicate that mammals’ occupancy tracks these changes in vegetation structure. However, the effect of fire was not consistent among species. We found that fire may restrict (Didelphis marsupialis), promote (Zygodontomys brevicauda) or have no impact (Oecomys sp.) on the mammals’ distribution depending on how each species uses the strata that disappeared because of fire. These findings provide evidence toward wildfire prevention for biodiversity conservation in fire-sensitive ecosystems of northern South America.