India being highly populated and developing country, the demand for various alternative fuel is increasing drastically. It is driven by the need to reduce dependency on traditional fossil fuels & reduce impact on environmental issues like Greenhouse gas, emissions & pollution. The potential options, CNG (Compressed Natural Gas) & Bio-diesel which are becoming increasingly popular and important. Biodiesel, a renewable fuel which is produced from waste materials & crops which grown repeatedly & easily available while CNG is more sustainable than diesel as natural gas is a cleaner-burning fossil fuel in comparison to coal or oil. This paper will focus on comparison between basic properties of Diesel, CNG & Bio- Diesel. In this study will also be focusing on survey of various Government initiatives, polices & infrastructural development which are evolving to encourage the usage of CNG & Biodiesel. These fuels are emerging as promising alternative contenders to traditional diesel. It has potential to reduce carbon footprints making them environmental friendly & more of sustainable energy options. This survey will also summaries the industry motivation from govt initiatives to promote the aim of cleaner transportation & its transition towards future sustainable energy. This study presents a comparative journey of CNG & Bio-diesel in India. Key parameters like, fuel properties, feedstocks and its availability, storage and handling, product integration, emissions and endurance performance assessments, customer acceptability etc. are considered for understanding these fuels in a better way. Also, it will highlight the key bottlenecks, technical challenges & the obstacles hindering the widespread adoption of Bio Diesel as compared to CNG. The paper also elaborates the challenges on sustainability of bio-diesel and CNG fuels and the futuristic opportunities in carbon neutral fuels like H2. The paper concludes with the comparative study of CNG & Bio-diesel on various aspects from ideation to execution.