With deteriorating energy reserves, (-)rising environmental apprehensions and-progressively more firm energy regulations have made renewable energy resources as an extremely attractive alternative source for near future. Biodiesel was considered as one of the promising energy resource for diesel engines. In the present work, non-edible oils namely pumpkin seed oil and Moringa oleifera oil were converted into methyl ester of Pumpkin seed oil (B1) and Moringa oleifera oil (B2) using transesterification process. The engine modification technique was said to be one of the current development in the field of the engine research motivating to achieve complete combustion. Two novel bowl geometries namely Toroidal Combustion Chamber (TCC) and Trapezoidal Combustion Chamber (TRCC) were developed and compared with standard Hemispherical Combustion Chamber (HCC). Further, the work was progressed to exergy and energy analysis. Amongst the bowl geometries, TCC showed better engine characteristics than TRCC and HCC. High swirl and squish behaviour of TCC engine helps in better air-fuel mixing and leads to complete combustion. Biodiesel samples contain oxygen molecules in its structure, reduced engine exhaust emissions except NOx were observed. On the whole, B1 may be considered as the promising alternative fuel as it exhibited 66.51% of exergy efficiency in TCC engine. (C) 2019 Elsevier Ltd. All rights reserved.