Understanding the effects of variation in resource availability and habitat disturbance on the ecology of mammals is vital for successful conservation management. In this study, we examined how human disturbances, resource availability and elevation gradients influence mammal assemblages in both managed coffee forest and natural forest of the Belete-Gera National Forest Priority Area, southwestern Ethiopia. We surveyed mammals using motion-detecting infrared camera traps in 90 locations for a total of 4142 camera days. We measured distance from main roads and settlements as disturbance factors, and distance from water sources, key grazing sites, and forest edges and woody plant diversity as resource variables. We assessed the mammal assemblages in coffee forest and natural forests using generalized linear models. Further, we used linear modelling to compare the relationships of mammal detection rates by feeding guilds and body size to resource variables. In total, we recorded 8815 videos identifying 23 different mammal species. The mammal assemblages in coffee forests were negatively associated with increasing distances from key grazing sites, water sources, and elevation. In contrast, the association with increasing distance from the road and woody plant diversity was positive. In addition, herbivores and large (25–200 kg) and very large (≥200 kg) mammals, were all negatively associated with increasing distance from the natural forest edges. With the conversion of natural forest to coffee forest and the intensification of coffee forest management, sustainable management of key grazing sites, water sources, and diverse woody plant species will be essential to the conservation of mammals. In addition, to ensure mammal conservation, adjacent natural forests around coffee forests should also be protected.