This presentation illustrates and discusses the relevance of coupling together metabolism and comparative agriculture approaches for the study of transitions in agriculture, based on two Indian case-studies. In the first case-study, located in Gujarat, we focus on the nitrogen flows and greenhouse gas emissions, which are both influenced by the low level of integration between crops and livestock. The second case-study, in Andhra Pradesh, deals with the increased consumption of fossil energy and the territory's fragile water balance, which could become negative if the trend towards planting more irrigated orchards continues. Both case studies account for the social diversity of farmers, livestock keepers and agricultural workers, therefore highlighting the patterns of coexistence between these categories. We show how crucial social diversity is for understanding what changes could be implemented, by whom and why. Another major asset of this work is that it combines scales of analysis (plot/herd, farm, territory) and several assessment criteria (environmental, social and economic), therefore providing a comprehensive overview of agricultural transitions.