Biodiesel is one of the renewable and eco-friendly fuels which can alleviate the concerns associated with fossil such as fluctuating prices and disastrous effects on the environment including global warming. The biofuel is usually produced from transesterification of vegetable oils and consists of alkyl esters. The chemical method of producing biodiesel has several drawbacks while the use of edible vegetable oils for biodiesel raises several concerns such as food vs. fuel crisis. The current work investigated biodiesel production from non-edible Salvadora persica seed oil (SPSO) and crude coconut oil (CCO) catalyzed by Burkholderia cepacia lipase in a solvent-free system. The biodiesel yield produced from these feedstock was compared and the effect of acyl acceptor (ethanol) in different ratios on biofuel production was determined. The fatty acid composition of SPSO and CCO was determined through gas chromatography and their average molecular weight was calculated. Different molar ratios of oil and ethanol were employed in transesterification for biodiesel production at 50?C, 7.0 pH with 50 mg lipase. Thin layer chromatography of oils and biodiesel samples was performed while the percentage yield was determined through gas chromatography. The results showed that medium chain fatty acids make up to 53.88% and 76.89% of the fatty acid content of SPSO and CCO respectively. Both are good candidates for enzymatic transesterification to produce medium chain biodiesel. The species of Salvadora persica (Pilu) has potential of a biodiesel crop. The average molecular weight was calculated as 749.53 g/mol for SPSO and 664.57 g/mol for CCO. Maximum biodiesel yield (around 70%) was obtained at 1:4 oil to ethanol molar ratio from both oils followed by a gradual decline at higher ratios. The gas chromatographic analysis of Salvadora biodiesel at 1:4 molar ratio showed that the yield of individual esters was mostly of medium and long chain fatty acids. In contrast the analysis of coconut biodiesel revealed that it consists mainly of the esters of medium chain fatty acids. Burkholderia cepacia lipase is a promising biocatalyst for production of biodiesel from SPSO and CCO provided the right conditions including optimum oil to ethanol molar ratio. Since free lipase was used in this study, stable yields of biodiesel as well as of individual fatty acid ethyl esters would have been achieved if any form of immobilized lipase would have been used.