The effect of a "controlled temperature" approach was investigated in the microwave-enhanced simultaneous extraction and transesterification of dry algae. Experimental runs were designed using a response surface methodology (RSM). The process parameters such as dry algae to methanol ratio, reaction time, and catalyst concentrations were optimized to evaluate their effects on the fatty acid methyl ester (FAME) yield under the "controlled temperature" conditions. Thermal energy associated with the microwave transesterification process was calculated at various temperature levels using the optimized process parameters. Algal biomass characterization and algal biodiesel analysis were carried out using various analytical instruments such as FTIR, TEM, GC-MS and confocal laser scanning microscopy. Thermogravimetric analysis under both nitrogen and oxygen environments was performed to examine the thermal and oxidative stability of the algal fatty acid methyl esters. (C) 2013 Elsevier Ltd. All rights reserved.