Toward a methodology for explaining and theorizing about social-ecological phenomena

•Case comparison and synthesis methods are increasingly being used alongside in-depth case studies to investigate causal effects and causal mechanisms in social-ecological systems (SES).•The potential of agent-based modelling (ABM) for developing generative explanations and building theory has recently been highlighted across several natural and social sciences.•Combining generalizing from case studies with ABM allows building and testing empirically grounded, generative explanations of phenomena in social-ecological systems that take emergence, complex causation, and context into account.•We propose a four-step abductive, collaborative, and transdisciplinary methodology for explanation and middle-range theory building.