This work presents an approach for the model-based design of a load-flexible fixed-bed reactor for performing the partial water-gas shift (WGS) reaction in the gas cleanup section of a coal-to-methanol plant. Three optimization problems with various combinations of objective functions (H-2/CO ratio, pressure drop, and operating costs) are formulated and solved using the nondominated sorting genetic algorithm (NSGA-II) to obtain the Pareto-optimal fronts, and the selected solutions are subjected to dynamic stability analysis. The optimum values of decision variables such as the weight of the catalyst, catalyst particle size, ratio of the reactor length and diameter, feed gas temperature, and steam to CO ratio are estimated and are found to be dependent on the choice of the objectives and tolerable deviation from their required values. The dependence of the H-2/CO ratio on the inlet gas temperature varies with the choice and combination of the objectives. In contrast, higher values of the steam to CO ratio (S/C) are associated with a lower deviation from the desired H-2/CO ratio for all three cases. However, optimum values of S/C are found to be below 1:1 because of its effect on the pressure drop and operating costs. The solutions obtained in the equilibrium-limited regime are found to be more stable in the presence of fluctuations in the feed flow rates but show intermediate stability with fluctuations in the inlet gas temperature. Four designs are recommended as the feasible designs, and the criteria of their application are discussed. Even though the work is related to a WGS reactor, the methodology used can be applied for the design of any other reactor system operating under variable feed conditions.