We studied production of biodiesel from microalga Chlorella protothecoides (SAG 211-10 C) through direct saponification of its wet biomass (70% moisture) in a microwave reactor using ethanolic potassium hydroxide. The resulting soap was precipitated by “common ion effect” using saturated solution of potassium chloride and subjected to simultaneous acidulation and esterification to form biodiesel. The optimum parameters for saponification were: Temperaure-60 °C, Ethanol to dry biomass ratio (ml/g)-80 : 1, concentration of KOH-0.5%, microwave power-450W; and for esterification they were Temperature-60 °C, wt% of sulfuric acid-2.5%, molar ratio of methanol to fatty acids-70 : 1, microwave power-450W. The kinetics and thermodynamics of saponification and esterification were investigated. Both reactions were found to follow pseudo-first-order kinetics. Activation energies were determined as 14.177 kJ/mol and 17.234 kJ/mol for saponification and esterification, respectively. The final biodiesel yield and purity were 98.74% and 94.83%, respectively.