There is a growing interest in multi/inter/transdisciplinary (MIT-D) work, which requires increasing levels of knowledge and co-production interaction. Many studies have addressed this theme with different approaches such as the nature of transversal scientific subjects, the concept of knowledge integration, and the dynamics of research groups to work consistently in collaboration. These are critical factors, particularly to government agencies responsible for assessment and funding researchers, research teams, or graduate courses. In this article, we propose a systemic MIT-D framework to graduate courses and research team's assessment. It takes into account the historical and current research in graduate courses assessment and a national graduate assessment system grounded on peer review and descriptive information conducted by a Brazilian public agency. The framework has three levels of analysis, allowing participation of multiple decision makers, using different approaches to explore four analytical dimensions (individual abilities, collaboration, content, and outputs/outcomes). We have analyzed its applicability in scientometric approaches and research assessment conducted by governmental agencies. The proposed framework is suitable and broadly relevant for both researchers and decision makers for analyzing courses and research teams.