Differences in system boundaries and problem framings are unavoidable in multi-organisational decision-making. Unstructured problems, such as the grand challenges, are characterised by the existence of multiple actors with different perspectives and conflicting interests, and they require a coordinated effort from multiple organisations. Within this context, this paper aims to understand stakeholders’ perceptions of system boundaries and problem framings, and their potential effects on decision-making by systematically comparing different stakeholder groups’ causal maps around the same shared concern. Bridging notions from Operational Research, System Dynamics and Organisational Studies, the comparison is based on a novel type of thematic analysis of Causal Loop Diagrams (CLDs) built with each stakeholder group on their perceptions of a given system. The proposed integrated approach combines qualitative with quantitative analysis, such as the centrality of the variables and the structure of the CLDs. Such CLDs comparison provides an intuitive way to visualise differences and similarities of the thematic clusters of variables, underlining factors influencing the shared concern. This could be considered a starting point for more shared understanding as well as more integrated holistic perceptions of the system and, consequently, a more systemic decision-making. Furthermore, for the sake of replicability, this paper also presents a qualitative participatory System Dynamics modelling process aimed to define the key aspects of a problem for each group of stakeholders to support a collaborative multi-organisational decision-making process. The research is based on the activities carried out for an urban regeneration case study in Thamesmead, London, United Kingdom