The interrelationships between smallholder agriculture, forest cover, and biodiversity loss have received insufficient research and analytic attention, though they stand at the center of the ongoing biodiversity crisis in tropical landscapes. Despite important advances in conservation science, knowledge generation remains fragmentary, and the formal institutions concerned with agriculture, forestry, social change, and climate change continue to work to a large extent in isolation, especially in developing countries. Drawing on our research program in the montane Eastern Himalaya of India, for example, two questions are explored: What types of landscapes can provide livelihood security for growing populations while maintaining healthy ecosystems? What kinds of knowledge, institutions, and policies will help us move toward land-use patterns that support livelihoods and protect biodiversity, given a regional economy based on small-scale agriculture? Here, we advocate for a greater integration of knowledge types (scientific, traditional, and participatory) and institutions (formal and informal, government and community) to foster better planning in order to reconcile several functions at the landscape level, including smallholder agriculture, the production of ecosystem goods and services, and the protection of biodiversity.