The Indian agriculture is facing problems of high input cost, deterioration of agro-ecosystems, poisoning of water, air and food bowls and farmers’ distress in spite of huge increase in the productivity of the cereals and other commercial crops due to adoption of the green revolution and successive agricultural technologies. The climate change caused disasters and uncertainty in crop productivity due to varied reasons are increasing day by day. The increasing size of farmer families with decreasing land holdings, poor socio-economic status and deteriorated agro-ecology have made farming as a most problematic profession in comparison with service sector, organized employment and business modules. The young generation of farmers are moving towards cities and metros as daily wage labourers. It appears that the technology transfer and outreach programs for the development of rural economy and agriculture as a profession could not achieve the desired goals. Henceforth, we need to deliberate and investigate the interwoven complexities of the farming, rural development and food security to have a sustainable food security and development of the rural areas, and villages as a green habitat for the large number of rural population, animals, plants and microbes. We can design and develop novel below ground and above ground agro-ecosystems for the emerging economic and nutritional needs of the farmers and entrepreneurs, ecosystem services and to reduce the increasing man-animal conflicts. It will require a new developmental pathway and carbon economy suitable for Indian conditions and novel innovations in agricultural production, storage, processing and marketing with its all possible backward and forward linkages.