Integrated natural resources management (INRM) has to address both the livelihood goals of farmers and ecological sustainability of agro-ecosystems and natural resources. Under the Ecoregional Initiative for the Humid and Sub-Humid Tropics of Asia-Ecor(I)Asia-one major set of activities has been the development of approaches, methodologies, and tools to meet the challenges of INRM research for sustainable agricultural development. Examples provided illustrate the role of these methodologies in the three main phases of knowledge development for improving INRM impact: knowledge generation, knowledge capitalization, and knowledge mobilization. The methodologies are designed for better integration across disciplines, spatial scales, and hierarchical levels of social organization. Attempts are made to quantify trade-offs between biophysical sustainability and socioeconomic considerations. The case is made for using these methodologies in a more complementary manner to help bridge the top-down and bottom-up approaches in INRM. Inherent in developing and implementing of these methodologies is the forging of partnerships and fostering linkages with multiple stakeholders as well as using the knowledge base and integrative tools as communication platforms.