The use of water-processable nanoparticles (WPNPs) is an emerging strategy for the processing of organic semiconducting materials into aqueous medium, dramatically reducing the use of chlorinated solvents and enabling the control of the nanomorphology in OPV active layers. We studied amphiphilic rod-coil block copolymers (BCPs) with a different chemical structure and length of the hydrophilic coil blocks. Using the BCPs blended with a fullerene acceptor material, we fabricated NP-OPV devices with a sustainable approach. The goal of this work is to clarify how the morphology of the nanodomains of the two active materials is addressed by the hydrophilic coil molecular structures, and in turn how the design of the materials affects the device performances. Exploiting a peculiar application of TEM, EFTEM microscopy on WPNPs, with the contribution of AFM and spectroscopic techniques, we correlate the coil structure with the device performances, demonstrating the pivotal influence of the chemical design over material properties. BCP5, bearing a coil block of five repeating units of 4-vinilpyridine (4VP), leads to working devices with efficiency comparable to the solution-processed ones for the multiple PCBM-rich cores morphology displayed by the blend WPNPs. Otherwise, BCP2 and BCP15, with 2 and 15 repeating units of 4VP, respectively, show a single large PCBM-rich core; the insertion of styrene units into the coil block of BCP100 is detrimental for the device efficiency, even if it produces an intermixed structure.