PurposeInterdisciplinary inquiry has been increasingly adopted to address issues of growing complexity in the biophysical and social sciences, as for example in agricultural research and rural development. The purpose of this article is to trace the origins of a Postgraduate Programme in Agroecosystems (PGA) in Brazil in order to discuss how its interdisciplinary practices have been enacted and epistemologically and institutionally constrained in just over 25 years of teaching and research activities.Design/methodology/approachConceptualized as a systemic inquiry, the study reported here builds upon participant observation, empirical evidence and literature-based analysis.FindingsSome of the academic features of the PGA introduced to facilitate interdisciplinary integration are presented and discussed, as well as their main challenges and obstacles, notably those emerging from “disciplinary imperialism” hindering individuals to work towards interdisciplinary inquiry and collaborative learning.Originality/valueRaising epistemological awareness and building systems literacy are critical aspects to be addressed to foster the embodiment of interdisciplinary inquiry practices. This might also lead to new understandings and to new and productive forms of joint teaching and research practices, fostering interdisciplinary integration.