In the present study, we report on an optimized method for fatty acid methyl esters (FAME) production from castor and jatropha seeds. In order to identify the most effective biodiesel production method, we have compared three two-stage methods, each consisting of oil extraction (the first step) and FAME production by transesterification (the second step), with the same three techniques each conducted in one stage, i.e., direct transesterification. The three techniques are conventional heating, sonochemistry, and microwave radiation. The FAME product was analyzed by 1H NMR spectroscopy and GC-MS. The SrO catalyst was reused successfully, together with seeds containing oil residues, for 10 cycles. The highest yield of FAME, 57.2 % of the total weight of the castor seeds, and a conversion of castor oil to FAME of 99.95 % were achieved in a one-stage method lasting 5 min using microwave radiation as a heat source. Using jatropha seeds leads to a yield of 41.1 % and a 99.7 % conversion of triglyceride to FAME under microwave irradiation in a one-stage method. The direct transesterification by sonication resulted in yields of 48.2 % and 32.9 %, and a 93.6 % conversion from castor and jatropha seeds, respectively.