Fluorination of alkyl groups is a known strategy for hindering miscibility, thus promoting phase separation, when blends are prepared with a hydrocarbon compound. A new perylene bis(dicarboximide) derivative functionalized with branched N-perfluoroalkyl moieties (BPF-PDI) has been synthesized as electron acceptor to be potentially used in conjunction with the electron donor hexakis(dodecyl)hexabenzocoronene (HBC-C 12 ) in bulk heterojunction solar cells. Aiming at controlling self-assembly between the two components at the supramolecular level, stoichiometric blends in CHCl 3 have been prepared either by spin-or drop-casting onto silicon surfaces, and further subjected to solvent vapour annealing (SVA) treatment in a CHCl 3 -saturated atmosphere. Spectroscopic investigation in solution shows the formation of supramolecular BPF-PDI-HBC-C 12 dimers, with an association constant K ass ¼ (2.1 AE 0.3) Â 10 4 M À1 , pointing to a strong and unexpected affinity between the two species within the mixture. Characterization through optical and atomic force microscopies of the deposited samples revealed that the self-assembly behaviour of the blends on SiO x is remarkably different from mono-component films, thus confirming the absence of a macroscopic phase-separation between the two components featuring isolated domains of the neat acceptor or donor compound. In addition, X-ray studies provided evidence for the existence of a local-scale phase separation. These findings are of importance for organic photovoltaics, since they offer a new strategy to control the phase separation at different scales in electron acceptor-donor blends.