This paper aims at analysing the effect of implementing a long-term STEM-based active learning course on students' motivation. First of all, a course that introduces science, technology and engineering concepts to students was designed. The key point was to provide the students with authentic learning activities based on real-world problems. The students had to solve those problems working in 3-members group. The teacher's role was as a learning guide. The course was implemented in a 6th grade class (primary education) and in a 7th grade class (secondary education) throughout a whole academic year. The Instructional Materials Motivation Survey (IMMS) was used to measure the students' motivation in two different moments: at the end of the first term and at the end of the third term. The IMMS is based on the ARCS Model and measures four motivational factors: attention, relevance, confidence and satisfaction. The high scores obtained in the IMMS manifest that most students were motivated with the STEM course. Indeed, the highest scores were obtained in the questions corresponding to the satisfaction factor. Furthermore, results evidence that the level of motivation varied only slightly from the first to the third term test. Hence, we can affirm that the hands-on learning activities proposed during the STEM course allow to create a learning experience that interests and engages students. Finally, obtained results allow to know how the students feel about the new STEM course and to redesign it, if necessary, in order to improve the studied motivational factors.