A method of biodiesel production from the freshwater microalgae Chlorella vulgaris based on the conversion of the dewatered algal biomass from a foam column (“foamate”) was investigated. The foam column collected and concentrated the microalgae. The foam was generated by passing air through a pool of algae, to which a collector/surfactant cetyltrimethylammonium bromide (CTAB) had been added. To produce biodiesel, the resultant “foamate” was esterified in situ using sulfuric acid and methanol. The effect of reaction temperature (30–70 °C), reaction time (30–120 min) and methanol/oil molar ratio (100–1000), were examined in a single-stage extraction–transesterification experiment on biodiesel yield at concentration of the catalyst H2SO4/oil molar ratio of (8.5/1). The thermodynamics and kinetics of transesterification of the microalgae oil were also investigated. The maximum biodiesel yield (96 ± 0.2%) was obtained at a reaction temperature of 70 °C, a reaction time of 90 min and methanol/oil molar ratio of 1000/1. Reaction kinetic parameters were determined that fitted the experimental data at all temperatures. A reversible reaction with first order forward and second order backward kinetics were found to be a good match for the experimental results. The kinetic model fitted experiments well under various temperatures and methanol/oil mole ratios. Under the most suitable conditions of reaction temperature, reaction time and methanol/oil molar ratio, the apparent activation energy was found to be 18.7 kJ/mol and pre-exponential factor 51.4 min−1. The activation entropy (ΔS), change in Gibbs free energy (ΔG) and variation in activation enthalpy (ΔH) revealed that the transesterification reaction is endergonic and unspontaneous, while the endothermic nature of the reaction was confirmed by the positive value (16.6 kJ/mol) of the ΔH. The thermodynamic information and kinetic model reported here will provide valuable insight into the understanding of the in situ transesterification process from algae foamate to biodiesel.