Net zero energy building design methodologies include integrative approaches and numerical tools to provide optimal performance and cost-effective results. Team integration, characterized by knowledge transfer between disciplines, has yet to be quantified for the design processes of these buildings. This article proposes a specific methodology for designing net zero energy buildings, tested through a case study design process conducted in an academic setting at Universidad Centroamericana in El Salvador, with the participation of students and faculty members. Through a survey, interdisciplinary knowledge transfer between team members was measured. We found that, without additional instruction, team participants outperformed a control group without project involvement by 16.4% (P < 0.002, t-test) in terms of interdisciplinary knowledge. This result implies that designers acquire new knowledge from other disciplines by interacting and solving design problems, although such acquisition is not uniform between disciplines. Remarkably, results show that the disciplinary groups that acquired the most knowledge about each other are Mechanical Engineering students and Architecture students. These results help us understand how to improve the design process, limit boundaries for disciplinary interactions, and determine which specific knowledge gaps to target per discipline in engineering and architecture education.