The purpose of this contribution is to lay down a preparatory groundwork for an ontology of ecosystem services in the setting of agroecosystems viewed as social-ecological systems. This ontology aims at defining a set of representational primitives with which to model agroecosystems, through the prism of ecosystem service flows to and from agriculture. It helps delineate between biophysical structures, processes, functions, and ecosystem services. On the human side of agroecosystems, the ontology includes a conceptualization of the behaviors that govern the management of ecosystem services at different levels. It strengthens the existing analytic basis of multidisciplinary research on ecosystem services in agroecosystems by prompting modelers to stick to a homogeneous dynamic-system decomposition of the target agroecosystem. Most importantly, it provides the conceptual link between biophysical research on ecosystem services and equally important considerations on cognitive and social aspects involved in agricultural and landscape-level decisions that aim at implementing agroecological principles.