The efficiency of organic solar cells with donor polymers and non-fullerene acceptors depends on a complex morphology. Similar chemical and electronic structures impede generating in-depth insights in morphological details. We visualise molecular arrangements and the nanomorphology in PBDB-T:ITIC blends by correlating transmission electron micrographs and material distribution maps. Material phases are identified by machine learning on hyperspectral data from electron spectroscopic imaging. We observe a specific polymorph of ITIC after thermal annealing. During annealing, enhanced by the presence of additives, PBDB-T acts as nucleation site for ITIC due to strong p-p-interactions of the electron withdrawing groups of both molecules. This leads to efficient charge transport paths in ITIC phases with direct p-p-contact to PBDB-T at the interface. We conclude that p-p-stacking between donor and acceptor molecules facilitates charge carrier generation within mixed interface regions. Broader context A crucial step for the advancement of organic solar cells was made by introducing novel, versatile non-fullerene molecules. These materials still provide specific advantages, such as solution processing, or strongly reduced toxicity in processing and use. However, the nanoscale structural landscape that determines performance and understanding of photophysics is still not fully known. Elucidating this relation by applying electron microscopy (EM)-one of the major tools offering the required resolution-is hampered by the similarity of donor and acceptor molecules regarding chemical composition and electronic structure. We demonstrate that analytical EM enables materials phase identification at the nanometer scale. Interpretation of morphological details is augmented by correlating phase distribution maps with high-resolution information about crystallinity. Using the system PBDB-T:ITIC we experimentally show that ITIC acceptor molecules adopt the periodic spacing of the PBDB-T repetition units. This happens already in mixed interface regions and is facilitated by polymorphism of ITIC. Here, we demonstrate that these visualized crystallites only form under thermal treatment in the presence of PBDB-T. We were able to correlate these structural features to improved performance. We envision an in-depth understanding of both the influence of processing parameters and the relation between molecular structure and photophysics.