The European Higher Education Area (EHEA) proposes to enhance active learning and student protagonism in order to improve academic performance. In this sense, different methodologies are emerging to create scenarios for self-regulation of their learning. In this study the cooperative, collaborative and interdisciplinary learning methodologies were compared in Spanish universities. The main objectives were to evaluate their effects in higher education and to explore the relationship between perceived group cooperation and self-perceived ability to work in a group, differences between educational Spanish contexts, educational methodologies and gender. To this end, a quasi-experimental design was carried out. Data analysis included the descriptive metrics, correlations and analysis of variance to evaluate the differences among pedagogical methods, their effects on cooperative learning, teamwork outcomes and gender differences, comprising a total of 229 students in Spain from Psychology, Early Childhood Education, Primary Education and Computer Engineering completed the two questionnaires. Results showed that the highest correlation between perceived cooperative activity and self-perceived ability to work in a group was found among computer science students, especially among women, suggesting that the interdisciplinary learning focused on software tool development may be the most effective methodology to improve teamwork and cooperative learning outcomes. Despite these findings concern only to Spanish universities, limiting the generalizability of results, the interdisciplinary methodology seems promising for improving both teaching quality and teamwork skills. The learning methodologies of interdisciplinary projects may therefore need to be implemented within the framework of cooperative and collaborative methodologies.