The present study aims to enumerate the issues of biodiesel supply chains in India. After an extensive literature review to access the current state of research on biodiesel, primary data was collected from academic experts and industry professionals engaged in biodiesel research and production. Ten issues were identified by the experts and pairwise rating of these issues were also done by the same experts. The issues were prioritised using the analytic hierarchy process (AHP) method. The results of the AHP analysis revealed that issues such as seasonality, variability in yield, logistics, and storage are the major issues that have a bearing on the supply chain of biodiesel. The study also suggests implications for theory and practitioners and policy actors. The present work is unique in the sense that research on the issues of biodiesel supply chains in India is meagre.