The paper presents a critical analysis of the possibilities and limits of the Institutional Analysis and Development (IAD) framework, proposed by Elinor Ostrom and team, specially addressing the mutual relations between natural and knowledge commons. It results from an action-research project on the role of open science (OS) in development, carried out in the municipality of Ubatuba, on the North Coast of the State of São Paulo, Brazil, in 2015-2017. The work involved: systematizing the literature on the IAD framework; mapping and selecting literature representative of other theoretical and conceptual approaches; critically using and adapting the framework to the case studied. The project provided the opportunity to observe how these dynamics take place in a relatively small-scale (while heavily interconnected) context. While the IAD framework helped us to analyse the institutional, political, and governance issues affecting knowledge production and circulation, we observed the higher complexity of our action arena, shedding light on the fact that natural and knowledge commons are the two dimensions of the same “commoning” process.