AbstractA detailed understanding of the interaction between molecules and 2D materials is crucial to implement molecular films into next‐generation 2D material‐organic hybrid devices effectively. In this regard, energy level alignment and charge transfer processes are particularly relevant. This work investigates the interplay between a hexagonal boron nitride (h‐BN) monolayer on an Rh(111) single crystal and self‐assembled C₆₀ thin films. The influence of the corrugated topography and electrostatic surface potential originating from the h‐BN/Rh(111) Moiré superstructure on the electronic level alignment and charging characteristics of C₆₀ is being studied. A combination of scanning tunneling microscopy/spectroscopy (STM/STS) and a theoretical tight‐binding approach is used to gain insight into the C₆₀ bandstructure formation and electronic decoupling of specific C₆₀. This decoupling results from adsorption site‐dependent variations of the molecular energy level alignment, which controls the strength of intermolecular hybridization. The decoupling of specific C₆₀ enables the direct observation of single‐electron charging processes via STS and Kelvin probe force microscopy. The charging of the C₆₀ is enabled by combining two gating mechanisms: the electrostatic surface potential of the monolayer h‐BN/Rh(111) Moiré and the electric field of the STM tip.