Scientific disciplines have been primary units of epistemic and institutional differentiation in modern research systems, encompassing the specialization of scientists, disciplinary communication systems, discipline-oriented work organization, and discipline-aligned systems of quality control and rewards. In its contemporary outline, the institution of science fosters knowledge production within disciplinary boundaries while disincentivizing interdisciplinary research. Emphasizing organizational structures that accommodate interdisciplinary paradigms, we argue that evaluation systems able to assess research output transcending disciplinary boundaries are necessary to support inter- and transdisciplinary knowledge production. Transforming current evaluation systems requires a deeper understanding of scientific pluralism and a corresponding conception of epistemic diversity. Drawing primarily on arguments from decolonial theory and science and technology studies, we conceptualize epistemic and social diversity as intersecting dimensions in evaluating inter- and transdisciplinary research. Finally, with a particular focus on neuroscientific (inter-)disciplines, we reconsider how translating epistemic and social diversity into research evaluation practice can do justice to and potentially advance the plurality of inter- and transdisciplinarity.