Present work reports an optimized protocol for the production of biodiesel (methyl ester) through two stage process i.e., esterification and transesterification of Neem and Karanja oils. The effect of different parameters on the production of Neem and Karanja oil methyl esters were studied. The methyl ester with best yield and quality was produced in case of Neem oil Methyl Ester at 9:1 mole ratio and 1.5 wt.% of catalyst KOH the yield was 90% and Karanja oil Methyl Ester at 9:1 molar ratio and 1 wt.% of KOH catalyst the yield was 92%. It was noted that greater or lower the concentration of KOH or methanol than the optimal values, the reaction either did not fully occur or lead to soap formation. The quality of the two methyl esters was analyzed by using Gas Chromotography â€“ Mass Spectroscopy (GC-MS), Elemental analyzer and Fourier Transform- Infrared Spectroscopy (FTIR) and was compared with each other. CHNOS are found by using elemental analyzer and are compared with the biodiesel standards (ASTM D6751). Physico-chemical properties of the methyl esters were compared to that of petroleum diesel. The produced biodiesel was found to exhibit fuel properties within the limits prescribed by the American Standards for Testing Material (ASTM D6751). It was concluded that Karanja oil was more suitable than Neem oil for the production of methyl ester.