The uncertainty in crystallization kinetics is of major concern in manufacturing processes, which can result in deterioration of most model‐based control strategies. In this study, uncertainties in crystallization kinetic parameters were characterized by Bayesian probability distributions. An integrated B2B‐NMPC control strategy was proposed to first update the kinetic parameters from batch to batch using a multiway partial least‐squares (MPLS) model, which described the variances of kinetic parameters from that of process variables and batch‐end product qualities. The process model with updated kinetic parameters was then incorporated into an NMPC design, the extended prediction self‐adaptive control (EPSAC), for online control of the final product qualities. Promising performance of the proposed integrated strategy was demonstrated in a simulated semibatch pH‐shift reactive crystallization process to handle major crystallization kinetic uncertainties of L‐glutamic acid, wherein smoother and faster convergences than the conventional B2B control were observed when process dynamics were shifted among three scenarios of kinetic uncertainties. © 2017 American Institute of Chemical Engineers AIChE J, 2017