Bulk and nanoscale molybdenum trioxide (MoO3) has shown impressive technologically relevant properties, but deeper investigation into 2D MoO3 has been prevented by the lack of reliable vapor‐based synthesis and doping techniques. Herein, the successful synthesis of high‐quality, few‐layer MoO3 down to bilayer thickness via physical vapor deposition is reported. The electronic structure of MoO3 can be strongly modified by introducing oxygen substoichiometry (MoO3−x), which introduces gap states and increases conductivity. A dose‐controlled electron irradiation technique to introduce oxygen vacancies into the few‐layer MoO3 structure is presented, thereby adding n‐type doping. By combining in situ transport with core‐loss and monochromated low‐loss scanning transmission electron microscopy–electron energy‐loss spectroscopy studies, a detailed structure–property relationship is developed between Mo‐oxidation state and resistance. Transport properties are reported for MoO3−x down to three layers thick, the most 2D‐like MoO3−x transport hitherto reported. Combining these results with density functional theory calculations, a radiolysis‐based mechanism for the irradiation‐induced oxygen vacancy introduction is developed, including insights into favorable configurations of oxygen defects. These systematic studies represent an important step forward in bringing few‐layer MoO3 and MoO3−x into the 2D family, as well as highlight the promise of MoO3−x as a functional, tunable electronic material.