Sustainability and food security are the major challenges faced by third world countries for the past several decades. Most of the third world countries are also facing problems of climate change, increasing population, overexploitation of natural resources and resource degradation associated with rapid economic growth. Among the scientific and policy circles there are controversies in using inorganic chemicals and biotechnology for sustaining the agricultural production. There is no critical comprehensive review on sustainability of alternative farming systems and their relative advantages over conventional, chemicalized and hi-tech agriculture for decision making at various levels. This review tries to fulfill the knowledge gap in this vital sector. The first part of the review discuss the current status of agroecosystems, with emphasis on their threats in terms of food security, long term sustainability, impacts on ecosystem services and climate change. We also evaluate the ecological, economic, social and cultural sustainability of inorganic agriculture. This analysis points emerging issues such as environmental degradation, loss of ecosystem services, non-sustainability and threats to food security in the context of global population growth and climate change. Hence there is an urgent need for identifying potential alternative farming strategies to achieve long term sustainability and food security as indicated by several leading workers in the field.