This article approaches the counting of subgraphs, in terms of signature-type functionals defined over combinatorial Hopf algebras of graphs. Well-known algebraic identities that arise in the context of counting subgraphs are then captured by their character property and a type of "Chen's identity". While different notions of subgraphs (and homomorphisms) correspond to different combinatorial Hopf algebras on graphs, we will show that they are all isomorphic to a polynomial Hopf algebra. In addition, the isomorphy between the Hopf algebras can be realized by maps that respect the counting operations.