The surface sensitivity and lack of dielectric screening in two-dimensional (2D) materials provide numerous intriguing opportunities to tailor their properties using adsorbed π-electron organic molecules. These organic-2D mixed-dimensional heterojunctions are often considered solely in terms of their energy level alignment, i.e., the relative energies of the frontier molecular orbitals versus the 2D material conduction and valence band edges. While this simple model is frequently adequate to describe doping and photoinduced charge transfer, the tools of molecular chemistry enable additional manipulation of properties in organic-2D heterojunctions that are not accessible in other solid-state systems. Fully exploiting these possibilities requires consideration of the details of the organic adlayer beyond its energy level alignment, including hybridization and electrostatics, molecular orientation and thin-film morphology, nonfrontier orbitals and defects, excitonic states, spin, and chirality. This Perspective explores how these relatively overlooked molecular properties offer unique opportunities for tuning optical and electronic characteristics, thereby guiding the rational design of organic-2D mixed-dimensional heterojunctions with emergent properties.