In this paper, three different transesterification technologies, catalytic, enzymatic, and in situ transesterification, are examined and compared for the production of microalgal biodiesel through a comprehensive techno-economic analysis. Conceptual process designs are proposed, and process models to are developed using the commercial software of SuperPro Designer. Base case results showed that the lowest biodiesel production cost is achieved by the catalytic transesterification ($4.77/kg), followed by the in situ ($9.92/kg) and enzymatic transesterification ($12.53/kg). Additionally, a global sensitivity analysis is performed to identify the important parameters and variables with strong influences on the biodiesel production cost. Each process was shown to be sensitive to different factors with the extraction solvent cost for the catalytic transesterification process, and the transesterification reactant alcohol cost for the enzymatic and in situ transesterification processes, respectively, being the most important one. The analysis results presented in this work can provide some guidelines for the future development of microalgal biodiesel production processes implementing the transesterification process.