<p>The many biological processes that define cellular physiology depend on a vast network of biochemical reactions. Each of these reactions is initiated by the formation of a complex between the macromolecules and metabolites that are involved in the reaction. Biochemical studies suggest that these complexes exist and operate as <i>function wholes</i>, not as mere aggregative assemblies of their component molecules. The metaphysical question I ask in this paper is how such unity arises—what are the metaphysical foundations for such unity? To help in this analysis, I enlist the resources of three metaphysical systems: process-relational philosophy, Aristotelian-scholastic substance philosophy, and Ivor Leclerc’s philosophy of nature. While these systems all regard nature as inherently dynamic and relational, they account for the unity of complex entities in different ways. In the end, I advance a proposal for an ontology of biochemical complexes based on a synthesis of metaphysical positions inspired by the Aristotelian substance ontology of Thomas Aquinas and the process-relational ontologies of Nicholas Rescher, John Dupré, and Ivor Leclerc. Two features of this account emerge as critical: (1) The molecular entities comprising a biochemical complex are not actual, but possess virtual being; only the resultant complex is actual, and (2) The ontological unity of a biochemical complex arises from <i>relation</i>, which is defined as the dynamic interactions among the molecules that comprise the complex. Relation maintains the structural integrity of the resultant complex, sets it apart from its environment as an individual, and accounts for its becoming.</p>