The design of an effective plant-wide control strategy is a key challenge for the development of future continuous pharmaceutical processes. This paper presents a case study for the design of a plant-wide control structure for a system inspired by an end-to-end continuous pharmaceutical pilot plant. A hierarchical decomposition strategy is used to classify control objectives. A plant-wide dynamic model of the process is used to generate parametric sensitivities, which provide a basis for the synthesis of control loops. Simulations for selected disturbances illustrate that the critical quality attributes (CQAs) of the final product can be kept close to specification in the presence of significant and persistent disturbances. Furthermore, it is illustrated how selected CQAs of the final product can be brought simultaneously to a new setpoint while maintaining the remaining CQAs at a constant value during this transition. The latter result shows flexibility to control CQAs independently of each other.