Thematic case-based studies can be used by instructors to enhance critical thinking and knowledge in a holistic fashion, as well as improve students' cognitive and metacognitive processes. While case-based learning approaches have been long used in the teaching of business, law and medicine, they have yet to see widespread use in many engineering disciplines. Furthermore, empirical research on the effectiveness of case-based learning within engineering is still in its infancy. Herein, we describe the use and impact of case-based instruction implemented in a third-year undergraduate bioprocess engineering course at the University of Waterloo. The overall objective of our study was to link key concepts related to bioprocess engineering to "real-world'' bioprocesses through a series of tutorial modules and research projects tied together by a common thematic case. The developed case focuses on genetically engineered Escherichia coli for the production of biofuels, specifically 1-propanol. The intent was to provide the students (n = 94) with the opportunity to gain a deeper understanding of biological systems by linking traditional fields of bioprocessing to an emerging field such as synthetic biology while also immersing students into situations that they could encounter while working in industry. Our results suggest that a majority of the students felt that the case was engaging and that the small-group based problem-solving exercises helped their understanding of design principles relevant to bioprocess engineering.