Land-use change can have profound effects on forest communities, compromising seedling recruitment and growth, and long-term persistence of forests on the landscape. Continued forest conversion to agriculture causes forest fragmentation which decreases forest size, increases edge effects and forest isolation, all of which negatively impact forest health. These fragmentation effects are magnified by human use of forests, which can compromise the continued persistence of species in these forests and the ability of the forests to support the communities that depend on them. We examined the extent and influence of human disturbance (e.g. weedy taxa, native and exotic tree plantations, clearings, buildings) on the ecological status of sacred church forests in the northern highlands of South Gondar, Ethiopia and hypothesized that disturbance would have a negative effect. We found that disturbance was high across all forests (56%) and was negatively associated with tree species richness, density, and biomass and seedling richness and density. Contrary to expectation, we found that forests < 15.5 ha show no difference in disturbance level with distance from population center. Based on our findings, we recommend that local conservation strategies not only protect large forests, but also the small and highly used forests in South Gondar which are critical to the needs of local people, including preserving large trees for seed sources, removing exotic and weedy species from forests, and reducing clearings and trails within forests.