Let Man * denote the category of closed, connected, oriented and based 3-manifolds, with basepoint preserving diffeomorphisms between them. Juhász, Thurston and Zemke showed that the Heegaard Floer invariants are natural with respect to diffeomorphisms, in the sense that there are functorswhose values agree with the invariants defined by Ozsváth and Szabó. The invariant associated to a based 3-manifold comes from a transitive system in F 2 [U ]-Mod associated to a graph of embedded Heegaard diagrams representing the 3-manifold. We show that the Heegaard Floer invariants yield functorsto the category of transitive systems in a projectivized category of Z[U ]-modules. In doing so, we will see that the transitive system of modules associated to a 3-manifold actually comes from an underlying transitive system in the projectivized homotopy category of chain complexes over Z[U ]-Mod. We discuss an application to involutive Heegaard Floer homology, and potential generalizations of our results. Contents 1. Introduction 1.1. Statement of Main Results 1.2. Further Directions and Applications 1.3. Organization of the Paper 1.4. Acknowledgements 2. Background 2.1.