This research studies the efficiency of Flipped Classroom (FC) and Challenge-Based Learning (CBL) as an innovative methodology to facilitate the learning of concepts involving sustainability and the circular economy by higher education students. This study, conducted as part of various innovative education projects, was applied in different courses (Environmental Management, Environmental Engineering and Industrial Ecology) taught to different engineering majors (Degree in Geomatics and Survey Engineering and Master's Degree in Chemical Engineering) at the Universidad Politécnica de Madrid (Spain). The main aim is to enhance the environmental competences of students by means of unconventional learning, increasing the motivation, participation and grades of the students in the course. Our results indicate that, in general terms, the students rated the efficiency of the new learning methodologies as satisfactory; however, a more detailed analysis of the results reveals some aspects that need special consideration, such as an assessment of specific and cross-cutting competences, in addition to the lack of previous soft skills, such as teamwork, creativity and work planning.