The potential of agent-based modelling (ABM) for developing theory has been recognized, yet methodologies are lacking. Building theories of social-ecological systems is challenging because of complex causality, context-dependence, and social-ecological interdependencies. We propose an approach that addresses these challenges through combining case-based empirical research with ABM in a collaborative modelling process. In-depth empirical research is essential for identifying a puzzle and potential explanations thereof, and for recognizing context and social-ecological interdependencies. Collaborative model building and analysis enables careful abstraction and reflection, and allows further exploring and testing the emerging theory in dynamic contexts, leading to better-grounded and transparent assumptions and theories. We call this approach BIM (Being In the Middle) and articulate it through three features: contextually embedded, collaboratively abductive and empirically stylized. We highlight how BIM facilitates new interdisciplinary avenues for discovering social-ecological interdependencies, discuss how it can be applied and what challenges and frontiers lie ahead.