When designing a molecular electronic device for a specific function, it is necessary to control whether the charge‐transport mechanism is phase‐coherent transmission or particle‐like hopping. Here we report a systematic study of charge transport through single zinc‐porphyrin molecules embedded in graphene nanogaps to form transistors, and show that the transport mechanism depends on the chemistry of the molecule–electrode interfaces. We show that van der Waals interactions between molecular anchoring groups and graphene yield transport characteristic of Coulomb blockade with incoherent sequential hopping, whereas covalent molecule–electrode amide bonds give intermediately or strongly coupled single‐molecule devices that display coherent transmission. These findings demonstrate the importance of interfacial engineering in molecular electronic circuits.