The project‐based learning (PBL) methodology has proven to be a valuable pedagogical approach in engineering programs for decades. However, a significant gap remains in the application of such methodologies in the field of bioprocess engineering. This study addresses this gap by exploring the implementation and outcomes of innovative PBL methodology in the context of bioprocess engineering education. The educational innovation involved the study of a bioprocess at the industrial scale, which comprises the definition of the culture medium, the operational units of the process, the design of the bioreactor with the assistance of MATLAB software, and the performance of a techno‐economic analysis. The results over eight academic years (441 students) demonstrated consistently high average grades in case studies (8.9 ± 0.3 out of 10), indicating successful student navigation of PBL challenges. The students’ positive feedback highlighted the satisfaction and effectiveness of the methodology in promoting collaboration, enhancing comprehension, and preparing students for real‐world scenarios. Overall, this study provides valuable insights into the successful implementation of PBL in bioprocess engineering education, highlighting its potential for fostering active learning, practical skill development, and student engagement. These findings contribute to the growing body of literature on innovative pedagogical approaches in engineering education and underscore the importance of ongoing evaluation and refinement for enhancing student learning outcomes.