Chemical process systems often need to respond to frequently changing product demands. This motivates the determination of optimal transitions, subject to specification and operational constraints. However, direct implementation of optimal input trajectories would, in general, result in offset in the presence of disturbances and plant/model mismatch. This paper considers reference trajectory optimization of processes controlled by constrained model predictive control (MPC). Consideration of the closed-loop dynamics of the MPC-controlled process in the reference trajectory optimization results in a multi-level optimization problem. A solution strategy is applied in which the MPC quadratic programming subproblems are replaced by their Karush-Kuhn-Tucker optimality conditions, resulting in a single-level mathematical program with complementarity constraints (MPCC). The performance of the method is illustrated through application to two case studies, the second of which considers economically optimal grade transitions in a polymerization process.