This article examines how researchers who study inter- and transdisciplinary research practices conceptualise and navigate methodological choices. Drawing on science, technology and society (STS), we combined a meta-ethnography and semi-structured interviews with scholars engaged in investigating inter- and transdisciplinary research. Our analysis identifies four interrelated dynamic pairs: familiarity/exploration, systematisation/adaptability, transferability/contextualisation, and reflection/action, that shape methodological decision-making. Rather than viewing these as tensions, we argue they function as productive dualities guiding reflexive and context-sensitive research inquiry. The study underscores the importance of methodological awareness, documentation, and collaborative engagement in advancing the study of inter- and transdisciplinary research. There has, to date, been no systematised understanding of how methodological practices influence the investigation and support of inter- and transdisciplinary research and their impact. The article then contributes to STS and inter- and transdisciplinary scholarships, by offering a systematised understanding of how methodological practices influence the investigation and support of collaborative research and its impact.