Manganese, showing stable oxidation states spanning from +2 to +7, gives rise to a variety of oxides (MnOx) whose exploitation in several technological fields, such as energy conversion and storage, catalysis, sensing, environmental and biomedical engineering, is highly promising. Nevertheless, the chemical complexity and the structural richness of MnOx -involving mixed-valence and metastable species -make the correct identification by Raman spectroscopy challenging, further complicated by the laser sensitivity, the poor Raman activity, and the conflicting literature scenario. Moreover, a careful optimization of the material in terms of phase, structure, and morphology is highly desirable in view of the final application, where a precise control over the materials properties is essential. In this work, we discuss the capability of room-temperature pulsed laser deposition (PLD), followed by post-deposition thermal treatments, to successfully grow engineered and pure MnOx thin films, whose phase and morphology at the nanoscale can be totally decoupled and independently optimized. The detailed Raman characterization of these films enabled a clear identification of specific MnOx phases and poses the basis for the rationale of the MnOx Raman spectra. Starting from the same MnO PLD target, we obtained five different MnOx phases (i.e., MnO, Mn3O4, Mn2O3, amorphous MnO2, and α-MnO2) with tailored and tunable degree of porosity and crystallinity, by modulating process parameters like the O2 deposition partial pressure (vacuum -100 Pa), the type of substrate, and the annealing temperature (300-900 °C) and atmosphere (air/vacuum). The Raman spectroscopy reliability of the MnOx phase assignment was assessed by thoroughly investigating the impact of the exciting laser power, and it was further validated by energy-dispersive X-ray spectroscopy, X-ray photoemission spectroscopy, and X-ray diffraction, providing additional insights into the compositional properties and the crystalline structure.