Combining a precise sputter etching method with subsequent AlOx growth within an atomic layer deposition chamber enables the fabrication of atomically flat lateral patterns of SiO2 and AlOx. The transfer of MoSe2 monolayers onto these dielectrically modulated substrates results in the formation of lateral heterojunctions due to the interaction with alternating regions of SiO2 and AlOx, with the flat substrate topography leading to minimal strain across the junction. Kelvin probe force microscopy measurements show significant variations in the contact potential difference (CPD) across the interface, with AlOx regions inducing a 230 mV increase in CPD. Photoluminescence spectroscopy reveals shifts in spectral weight of neutral and charged exciton species across the different dielectric regions. On the AlOx side, the Fermi energy moves closer to the conduction band, leading to a higher trion‐to‐exciton ratio, indicating a bandgap shift consistent with CPD changes. In addition, transient reflection spectroscopy highlights the influence of the dielectric environment on carrier dynamics, with the SiO2 side exhibiting rapid carrier decay typical of neutral exciton recombination. In contrast, the AlOx side shows slower, mixed decay behavior consistent with conversion of trions back into excitons. These results demonstrate how dielectric substrate engineering can tune 2D materials, allowing scalable fabrication of advanced junctions for novel (opto)electronics applications.