Self-assembly of functional supra-molecular nanostructures is among the most promising strategies for further development of organic electronics. However, a poor control of the interactions driving the assembling phenomena still hampers the tailored growth of designed structures. Here exploration of how non-covalent molecule-substrate interactions can be modified on a molecular level is described. For that, mixtures of DIP and F16CuPc, two molecules with donor and acceptor character, respectively are investigated. A detailed study of their structural and electronic properties is performed. In reference to the associated single-component layers, the growth of binary layers results in films with strongly enhanced intermolecular interactions and consequently reduced molecule-substrate interactions. This new insight into the interplay among the aforementioned interactions provides a novel strategy to balance the critical interactions in the assembly processes by the appropriate choice of molecular species in binary supra-molecular assemblies, and thereby control the self-assembly of functional organic nanostructures.