Organic semiconductor materials exhibit properties that enable use in various electrical devices, such as organic solar cells and field-effect transistors. It is challenging, however, to control molecular packing at organic–organic interfaces and also characterize the morphology at buried interlayers. Here, we demonstrate via vertical physical vapor transport the ability to grow single-crystalline bilayer organic semiconductors on graphene using two small molecules: zinc phthalocyanine (ZnPc), and 3, 4, 9, 10-perylenetetracarboxylic dianhydride (PTCDA). We employ 4D-scanning transmission electron diffraction (4D-STEM) to directly observe the orientation distribution of ZnPc and PTCDA crystallites on graphene, explaining the different growth mechanisms of organic molecules on graphene substrates, and we predict the morphology of the stacked ZnPc/PTCDA heterojunctions. Graphical abstract: [Figure not available: see fulltext.]