This study analyzes self-perception in innovation competences development in engineering students with the objective of understanding how to better design educational strategies to improve innovation skills in future engineering graduates. The INCODE (Innovation Competences Development)-Rubric 5 survey is used to compare two groups of engineering students from Telecom Engineering school from UPC (Technical University of Catalonia) going through two types of project-based courses: CBI (Challenge Based Innovation) course versus PDP (Product Development Project) course. CBI is an innovative learning experience carried out by three institutions: Telecom Engineering School of UPC, ESADE Business School and IED Istituto Europeo di Design in collaboration with CERN, where mixed teams of students from the three institutions face open innovation challenges through Design Thinking, with the objective of designing solutions to complex societal problems, considering the use of CERN technologies if suitable. PDP is the ‘‘standard’’ capstone course taken by Telecom engineering students following a classical project-management approach. Results show that both courses give a good self-perception of the learning outcomes in the innovation-related skills, according to what is observed in the INCODE surveys’ results when comparing CBI and PDP. The differences found between CBI and PDP are small and only moderately deviated towards CBI in the individual competences dimension