Abstract The aim of this work is to argue for the idea that processes and process-based entities are to be modelled as relational structures. Relational structures are genuine structures, namely entities not committed to the existence of basic objects. My argument moves from the analysis of Whitehead’s original insight about process-based entities that, despite some residual of substance metaphysics, has the merit of grounding the intrinsic dynamism of reality on the holistic and relational characters of process-based entities. The current model of process ontology requires genuine emergence and this, in turn, requires organizations, i.e., emergence in organizations. Another view about processes rely on a structural specification of processes. I suggest that the two views can be made compatible by the help of a specific sort of structures, namely relational structures. The appeal to the mathematical theory of genuine structures, category theory, reveals the formal plausibility of this convergence. According to this formal approach, genuine structures are essentially dynamic entities for they are relational, namely, as well as organizations, they are not existentially committed to particulars.