Higher education institutions have to adapt to the rapid technological, cultural, economic and demographic changes that are taking place throughout the world. An example of educational innovation when applied for the first time and being innovative and generating changes is Project Based Learning (PBL), where the students are the protagonists of their teaching-learning process, and the application of this methodology allows them to face every day or real situations. The use of this PBL has turned out to be a novel institutional commitment, due to the organizational management of the teaching staff and the interconnection of different areas of knowledge of the curriculum. The main objective of this research is to analyze an interdisciplinary PBL experience of two academic years carried out in the Primary Education Degree at the University of Deusto (Spain). For this purpose, a qualitative analysis of 27 semi-structured interviews with the participating students was carried out. The results indicate as advantages of PBL the interdisciplinarity, giving solutions to a real case, the significant learning and the development of professional competences for professional performance such as active listening, teamwork, and leadership. However, they have indicated, as well, that they feel lost and unmotivated in the process, mainly due to the lack of teamwork skills, lack of knowledge of how to search for information, teachers’ lack of presence in class and the lack of connection between the subjects of the curriculum. Thus, as improvement strategies, they propose to carry out teamwork dynamics, to improve teacher coordination and to readapt the project (deliveries, workload and evaluation criteria, among others).