Process-relational perspectives have been proposed as new ways of conceptualising, analysing and engaging with social–ecological systems (SES) that are capable of dealing with intertwinedness and complexity. The application of PR perspectives in SES research, however, remains challenging and largely conceptual. We explore the possibilities of combining process-relational thought with agent-based modelling as a methodology for thinking with and exploring the becoming/emergence of SES. We call it relation-based modelling (RBM) and develop it through modelling the emergence/becoming of a virtual small-scale fishery. RBM focuses attention towards the apparatus, i.e. the material and discursive practices that shape the model structure which then provides the conditions for the emergence of fishery assemblages in a virtual, simulated world. Our attempt to produce a model from a process-relational perspective supported critical reflection of our assumptions about fisheries and agent-based modelling, particularly with respect to questioning common ways of dissecting the world that hinder understanding their intertwinedness and dynamism. Analysis of simulation results and our reflections about the apparatus together reveal how organisation at different levels, from the arrangement of practices that shape the design of the model to the arrangements of elements in the virtual world of the simulation influence the emergence of a virtual fishery. We reflect on the tensions we encountered when disentangling the entangled and formalising process-relational ideas and conceptualisations in the model and the learning and transformations that occurred through this process. A process-relational practice of modelling can open up possibilities to think differently about SES and change the way we theorise and act within them.