This study, undertaken in the Northwest USA, explores how graduate students in an interdisciplinary social-ecological systems research course engaged with concepts of epistemic difference and Indigenous knowledge as part of a required module titled "Ways of Knowing" to engage social and ecological change in climate science. We describe how graduate students engaged with Indigenous ways of knowing and discussion of interdisciplinary equity across knowledge systems and methodologies. Analysis of student perspectives drawn from fieldnotes, student course work, and post-course interviews illuminates tensions in preparing interdisciplinary science researchers to navigate epistemic difference. Students embraced Indigenous ways of knowing as useful for conceptualizing complex tensions in social-ecological systems research, while simultaneously sidestepping deeply rooted issues of power and coloniality in research. We trace two primary ways Indigenous ways of knowing informed interdisciplinary processes in students' conceptualizations of social-ecological challenges: Science as more expansive: Reflexivity and interpersonal dilemmas; and Grappling with power and settler colonial discomfort. We argue that continued engagement in epistemic difference, particularly Indigenous knowledges, is necessary for cultivating scientific engagement in complex notions of knowledge equity in climate sciences involving Indigenous peoples/lands. Finding underscore how changes in graduate research training can expand research imaginaries, however, such expansions need to be systematic and multi-stranded to interrupt the deep-rooted marginalization of non-Western knowledges in scientific research.