Some of the most critical competencies students need to acquire to become control engineers require performing practices under actual industrial conditions. This means that they must not only master the theoretical aspects of the discipline but also acquire skills and attitudes to face unpredictable real-world situations. Software tools such as Matlab/Simulink are widely used to train the design and validation of controllers, but they fail to provide real industrial contexts. Nowadays, there are 3D simulation tools that support recreating industrial environments to a remarkable extent, making them very attractive for university courses. Nevertheless, their application in engineering courses is scarce yet. This paper presents a methodological framework for seizing into competency-based courses one of these simulation tools, called Factory I/O. Our approach was evaluated in a master’s course on Industrial PID Control at Pontifical Catholic University of Valparaíso (PUCV) in Chile. The evaluation comprised the qualitative analysis of students’ grades over four consecutive course editions and the qualitative study of students’ opinion on Factory I/O educational value. The objectives of our evaluation were (i) testing if Factory I/O helped students develop skills hard to practice in academic contexts, such as detecting faults or recognizing the importance of having well-defined operation protocols; (ii) validating our methodology for competency-based courses; and (iii) surveying our students about Matlab/Simulink and Factory I/O strengths/weaknesses to teach control engineering. According to the results, (a) Factory I/O complements Simulink by providing an adequate virtual environment to learn the aforementioned skills; and (b) our methodology supports courses’ continuous improvement through the statistical analysis of students’ achievements at different abstraction levels.