Economic viability of biodiesel technology is at stake due to the high cost of edible oil feedstock and slow reaction rates due to limited solubility of oil in methanol. In situ transesterification of non edible oil seed particles can minimize the cost of feedstock. Microwave pretreatment of seeds can make oil molecules more reactive. Use of phase transfer catalysts can enhance the reaction rates. In the present work, these three concepts are utilized together to investigate alkaline in situ transesterification of microwave pretreated jatropha curcas seed particles in presence of benzyltrimethylammonium hydroxide (BTMAOH) as a phase transfer catalyst (PTC). It was observed that addition of PTC to alkaline catalyst has improved conversion and reduced reaction time. Microwave pretreatment of jatropha seed particles reduced reaction time drastically. The quality of biodiesel produced was within the limits of the international standard requirements of ATME D6751 and EN-14214. Thus, combined use of microwave pretreatment of seed particles, phase transfer catalysis in the presence of alkaline catalyst can increase the rate of in situ transesterification and product yield.