Aristotle has a metaphysics of individual substances, substrata persisting through time that are neither in nor said of a subject. That I do not dispute. However, when we move from the individual to the universal, from perception to knowledge, Aristotle has a metaphysics of relations. This I will try to sketch out here.
Aristotle appeals to abstraction at key places in his philosophy. Somehow abstraction gets us to the first principles and to the objects of the most fundamental sciences. Somehow universals are abstracted from singulars and have no transcendent existence.
Aristotle never states his theory of abstraction formally or too explicitly. Yet he surely uses it. Perception is the abstraction of forms from substances; knowledge is the abstraction of the universal from singulars; the objects of the mathematical sciences are “the things said from abstraction”. [An. III.4; Metaph. I.1; Phys. I.1] Likewise, he speaks of “cutting off a part of being” and making a science about it. [Metaph. 1003a24-5] Physics concerns substances qua movable; geometry considers substances qua figure. [Metaph. 1026a7-10; 1061a28-1062b11; 1077b22-1078a21] We start with the individual substances given in sense perception and then isolate aspects of them, the abstracta, for study in particular sciences. Above all, on account being abstractions, the essences of substances can be real without existing in their own right. Aristotle tends to express abstractions in the language of what later came to be called “reduplicatives”: something may be considered “qua this” or “qua that”. Yet he has not left us a treatise on abstraction. This lack of explicit doctrines I think accounts for many of the disputes over his ontology.
Abstractions have the formal features of relations. Aristotle appeals to these features in addressing the problem of universals.
Bäck, Allan, "Aristotle's Abstract Ontology" (2008). The Society for Ancient Greek Philosophy Newsletter. 377.