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Large-scale and air-stable two-dimensional metal layers intercalated at the interface between epitaxial graphene and SiC offer an appealing material for quantum technology. The atomic and electronic details, as well as the control of the intercalated metals within the interface, however, remain very limited. In this Letter, we explored ultrathin indium confined between graphene and SiC using cryogenic scanning tunneling microscopy, complemented by first-principle density functional theory. Bias-dependent imaging and tunneling spectroscopy visualize a triangular superstructure with a periodicity of 14.7 ± 3 Å and an occupied state at about −1.6 eV, indicating proof of highly crystalline indium. The scanning tunneling microscopy tip was used to manipulate the number of indium layers below graphene, allowing to identify three monatomic In layers and to tune their corresponding electronic properties with atomic precision. This further allows us to attribute the observed triangular superstructure to be solely emerging from the In trilayer, tentatively explained by the lattice mismatch induced by lattice relaxation in the topmost In layer. Our findings provide a microscopic insight into the structure and electronic properties of intercalated metals within the graphene/SiC interface and a unique possibility to manipulate them with atomic precision using the scanning probe technique.