Departing from the comprehensive reviews carried out in the field, we identify the key challenges that agent-based methodology faces when modeling coupled socio-ecological systems. Focusing primarily on the papers presented in this thematic issue, we review progress in spatial agent-based models along the lines of four methodological challenges: (1) design and parameterizing of agent decision models, (2) verification, validation and sensitivity analysis, (3) integration of socio-demographic, ecological, and biophysical models, and (4) spatial representation. Based on this we critically reflect on the future work that is required to make agent-based modeling widely accepted as a tool to support the real world policy. •Progress of agent-based methodology in modeling coupled socio-ecological systems.•Key methodological challenges for ABM.•Societal issues and critical reflection on the prospects of ABM.