The emergence of transformation as a core component in sustainability science and practice has opened an exciting space for transdisciplinary research. Yet, the mainstreaming of transformation has also exposed epistemological rifts between diverse research perspectives, presenting significant challenges for transdisciplinary teams. Using coral reef social-ecological systems as an example, we explore how these points of tension may be addressed using a three stage process: Firstly, promoting epistemological transparency, where different kinds of knowledge framings are made explicit; secondly, employing feedbacks as a bridging concept to effectively engage with complex system dynamics from multiple perspectives; and finally, encouraging plurality, rather than the unification of epistemologies, to foster innovative, diverse, and sustainable pathways during this formative moment for global environmental sustainability.