Farmers in the middle hills of Nepal have been abandoning agricultural land over the last three decades due to complex socio-ecological drivers and dynamics. A consequence of this shift is the succession of forest. Naturally regenerating tree species, and farmer’s opinions of species benefits, were assessed with field measurements and interviews to guide an analysis of the socio-ecological factors that influence forest succession. Non-linear patterns of species abundance and diversity suggest that intermediate regimes of disturbance lead to higher rates of biodiversity than either high or low management interference of regenerating forest patches. Farmers that practice no or low levels of disturbance exhibit little investment or perceived benefits from the subject land beyond occasional fodder collection, while high forest disturbance is motivated primarily by activities within the succeeding forest that generate income. Intermediate disturbance patterns in succeeding forests are similar in nature to livelihood practices within the traditional, small-scale rural farming systems in Nepal. These heterogenic agro-ecosystems are also associated with higher species diversity. The inferences from these observations suggest that while drivers of land abandonment and perceptions of succeeding forest species are a consequence of complex and interacting socio-ecological factors, the disturbance of regenerating forest is motivated by perceived benefits associated with low-labour alternative landuses, whether deliberate (high disturbance) or default (intermediate). Policy to support the maintenance or enhancement of forest succession in multi-functional landscapes could contribute to higher species diversity and resilience through transitioning landscapes in rural Nepal.