We report a didactic and simple example of the subtleness in the balance of intermolecular and molecule–substrate interactions and its effect on molecular self-assembly. The study is performed on two closely related molecular blends of copper phthalocyanines and pentacene, in each of which one of the two molecules is fluorinated. Reversing the fluorination brings about changes in the intermolecular hydrogen bonds, as well as in the interactions with the substrate. As a result, on Au(100) substrates one blend assembles into a crystalline structure, whereas the other, displaying weaker intermolecular interactions and a larger corrugation in the molecule–substrate interaction potential, results in a disordered layer. However, the difference between the two blend’s structures vanishes when substrates with less corrugated interaction potentials are used.