Molecular-scale manipulation of electronic/ionic charge accumulation in materials is a preeminent challenge, particularly in electrochemical energy storage. Layered van der Waals (vdW) crystals exemplify a diverse family of materials that permit ions to reversibly associate with a host atomic lattice by intercalation into interlamellar gaps. Motivated principally by the search for high-capacity battery anodes, ion intercalation in composite materials is a subject of intense study. Yet the precise role and ability of heterolayers to modify intercalation reactions remains elusive. Previous studies of vdW hybrids represented ensemble measurements at macroscopic films/powders, which do not permit the isolation and investigation of the chemistry at individual 2-dimensional (2D) interfaces. Here, we demonstrate the intercalation of lithium at the level of individual atomic interfaces of dissimilar vdW layers. Electrochemical devices based on vdW heterostructures comprised of deterministically stacked hexagonal boron nitride, graphene (G) and molybdenum dichalcogenide (MoX2; X = S, Se) layers are fabricated, enabling the direct resolution of intermediate stages in the intercalation of discrete heterointerfaces and the extent of charge transfer to individual layers. Operando magnetoresistance and optical spectroscopy coupled with low-temperature quantum magneto-oscillation measurements show that the creation of intimate vdW heterointerfaces between G and MoX2 engenders over 10-fold accumulation of charge in MoX2 compared to MoX2/MoX2 homointerfaces, while enforcing a more negative intercalation potential than that of bulk MoX2 by at least 0.5 V. Beyond energy storage, our new combined experimental and computational methodology to manipulate and characterize the electrochemical behavior of layered systems opens up new pathways to control the charge density in 2D (opto)electronic devices.