We demonstrate that small-molecule organic thin films of pentacene deposited from thermal and supersonic molecular beam sources can undergo significant reorganization under vacuum or in N₂ atmosphere, beginning immediately after deposition of thin films onto SiO₂ gate dielectric treated with hexamethyldisilazane (HMDS) and fluorinated octyltrichlorosilane (FOTS). Films deposited on bare SiO₂ remain unchanged even after extended aging in vacuum. The changes observed on low-energy surfaces include the depletion of molecules in the interfacial monolayer resulting in the population of upper layers via upward interlayer transport of molecules, indicating a dewetting-like behavior. The morphology of pristine, as-deposited thin films was determined during growth by in situ real-time synchrotron X-ray reflectivity and was measured again, ex situ, by atomic force microscopy (AFM) following aging at room temperature in vacuum, in N₂ atmosphere, and in ambient air. Important morphological changes are observed in ultra-thin films (coverage < 5 ML) kept in vacuum or in N₂ atmosphere, but not in ambient air. AFM measurements conducted for a series of time intervals reveal that the rate of dewetting increases with decreasing surface energy of the gate dielectric. Films thicker than ∼5 ML remain stable under all conditions; this is attributed to the fact that the interfacial layer is buried completely for films thicker than ∼5 ML. This work highlights the propensity of small-molecule thin films to undergo significant molecular-scale reorganization at room temperature when kept in vacuum or in N₂ atmosphere after the end of deposition; it should serve as a cautionary note to anyone investigating the behavior of organic electronic devices and its relationship with the initial growth of ultra-thin molecular films on low-energy surfaces.