Transdisciplinary (TD) sustainability science is increasingly applied to study transformative change. While only certain domains of the field explicitly adopt a transformative agenda, from a complexity worldview all researchers are part of, and thus intervening in, the transformations they seek to understand. Reflexivity is cited as a crucial capacity for navigating ‘research as intervention’. Yet, there is little attention to what reflexivity looks like and how it might be facilitated in service of transformation. Our objective was to establish a framework for reflexivity as a transformative capacity in sustainability science. We developed the framework through a rapid scoping review of literature on transdisciplinarity, transformation, and reflexivity (underpinned by critical systems theory), and refined the framework through reflection on a scenario study in the Red River Basin (US, Canada). The framework characterizes reflexivity as a dynamic, embedded, and shared learning process that manifests through interacting boundary processes (i.e., sources of selectivity): boundary delineation, interaction, and transformation. These processes can be facilitated in service of transformation, for example by decentring dominant boundaries to create open epistemic spaces. The case study reflection suggests how embedding this framework in research can expose boundary processes that block transformation and nurture more reflexive and transformative research.