Manganese oxides/oxyhydroxides (MnOx) are based on Mnn+O6 and Mnn+O4 polyhedra arranged such as to form compact, channel or layered structures. In geology, they are precious archives of past redox conditions for palaeoclimatic reconstructions; in material sciences, they are used for a variety of applications, from pigments to environmental remediation and energy storage. Thus, the fast, remote and non‐destructive identification of MnOx is critical in several disciplines. Micro‐Raman spectroscopy is often used for this purpose, although a systematic characterization of their stability under the laser beam is still lacking. In this work, we present our results on the behaviour of the most common MnOx having compact and channel structures when a 532‐nm laser with intensity between ~23 μW/μm2 and ~36.8 mW/μm2 is used. The compact structures of manganosite (NaCl‐like) and hausmannite (spinel‐like) are stable up to ~36.8 mW/μm2. The stability of oxides with channel structures depends on channel size, charge of channel cations and valence state of Mn. Hausmannite is the final degradation product of all MnOx with channel structures, irrespective of the starting phase. Pyrolusite, manganite, hollandite and romanéchite are relatively stable under the laser beam, and the transition to the spinel structure occurs above 2.5 mW/μm2 while the degradation of cryptomelane and todorokite starts ~226 μW/μm2. The analysis of MnOx thus needs very accurate experimental conditions to avoid misleading and incorrect phase identifications. Based on our data, we propose an analytical protocol for a proper characterization of these minerals via Raman spectroscopy.