Biodiesel transesterification reactors resemble the heart of ally biodiesel manufacturing plant. These reactors involve a highly complex set of chemical reactions and heat transfer characteristics. The high nonlinearity inherent in the dynamics of these reactors requires an efficient process control algorithm to handle the variation of operational process parameters and the effect of process disturbances efficiently. In this work, a multi-model adaptive control strategy is considered for achieving the goal mentioned above. In order to implement the adaptive controller, a rigorous mechanistic model of the biodiesel transesterification reactor was developed and validated with published experimental results. The validated model was analyzed for stability and nonlinearity. The analysis revealed that the system is stable. However, its high nonlinearity necessitates an advanced control strategy to be considered. The input-output relationship between the effective process variables was studied and the control system synthesis revealed a two-by-two control system. Two adaptive control loops were then designed and tuned to optimize the performance of the controller. Finally, a comparison with conventional controllers revealed the superiority of the new control system in terms of set-point tracking and disturbance rejection. The results of this work prove that an adequately designed adaptive control system can be used to improve the performance of the transesterification reactor.