The introduction of Quality by Design in the pharmaceutical industry stimulates practitioners to better understand the relationship of materials, processes and products. One way to achieve this is through the use of targeted experimentation. In this study, an optimization framework to design experiments that effectively leverage parameterized process models is presented to maximize the space covered in the output variables while also obtaining an orthogonal bracketing study in the process input factors. The framework considers both multi‐objective and bilevel optimization methods for relating the two maximization objectives. Results are presented for two case studies—a spray coating process and a continuously stirred reactor cascade—demonstrating the ability to generate and identify efficient designs with fit‐for‐purpose trade‐offs between bracketed orthogonality in the input factors and volume explored in the process output space. The proposed approach allows a more complete understanding of the process to emerge from a small set of experiments.