Interdisciplinary competence is important in academia for both employability and sustainable development. However, to date, there are no specific interdisciplinary education models and, naturally, no empirical studies to assess them. Since problem-based learning (PBL) and project-based learning (PjBL) are learning approaches that emphasize students' collaboration, both pedagogies seem suitable to enhance students' interdisciplinary competence. Based on the principle of constructive alignment and four instructional principles on interdisciplinary learning, this paper proposes that students profit more from interdisciplinary PBL (iPBL) than interdisciplinary PjBL (iPjBL). A pre-post study was conducted with a sample of 95 students participating in iPBL and 183 students participating in iPjBL. As expected, multilevel models on students' development in (a) interdisciplinary skills, (b) reflective behavior, and (c) recognizing disciplinary perspectives show that iPBL enhances students' interdisciplinary competence more than iPjBL.