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Agent-based models of land use and cover change (ABMs/LUCC) have traditionally represented land-use and land-cover changes as arising from social, economic and demographic conditions, while spatial ecological models have tended to simulate the environmental impacts of spatially aggregated human decisions. Incorporating a dynamic representation of ecosystem processes into ABMs/LUCC can enable new or counter-intuitive insights to be gained into why certain path-dependent outcomes arise and can also spatially constrain model processes, thereby improving the spatial fit of model output against observational data. A framework is therefore provided to assist in determining an optimal approach for representing ecological processes in an ABM/LUCC according to the research question and desired application of the model. Relevant challenges limiting the integration of complex, dynamic representations of ecosystem processes into ABMs/LUCC are then assessed, with solutions provided from recent examples. ABMs/LUCC that use a dynamic representation of ecological processes may be applied to investigate the complex, long-term responses of the coupled human–natural system to a variety of climatic shifts and ecological disturbances.