The understanding of the thermally induced phase transformations of molybdenum oxide nanostructures is relevant due to the direct impact that this type of additives would have in lubricant applications. We report on the evolution of phases in molybdenum oxide nanostructures studied by thermal-X-ray diffraction from room temperature up to 455 °C. The samples were grown by the gas condensation method using different atmospheres at low pressures. Information about morphological and structural characteristics of the as-prepared nanostructures were obtained by transmission electron microscopy and selected area electron diffraction patterns, respectively. Our results revealed the formation of porous nanostructures and the coexistence with crystalline, depending on the atmosphere. A detailed analysis on the thermal evolution of crystalline structure was performed for the α-MoO3 phase unit cell. Our results highlight that thermally induced processes must be considered in the design of tribological nanoadditives that contain molybdenum oxide particles.