Hybrid nanoparticles allow exploiting the interplay of confinement, proximity between different materials and interfacial effects. However, to harness their properties an in-depth understanding of their (meta)stability and interfacial characteristics is crucial. This is especially the case of nanosystems based on functional oxides working under reducing conditions, which may severely impact their properties. In this work, the in-situ electron-induced selective reduction of Mn₃O₄ to MnO is studied in magnetic Fe₃O₄/Mn₃O₄ and Mn₃O₄/Fe₃O₄ core/shell nanoparticles by means of high-resolution scanning transmission electron microscopy combined with electron energy-loss spectroscopy. Such in-situ transformation allows mimicking the actual processes in operando environments. A multi-stage image analysis using geometric phase analysis combined with particle image velocity enables direct monitoring of the relationship between structure, chemical composition and strain relaxation during the Mn₃O₄ reduction. In the case of Fe₃O₄/Mn₃O₄ core/shell the transformation occurs smoothly without the formation of defects. However, for the inverse Mn₃O₄/Fe₃O₄ core/shell configuration the electron beam-induced transformation occurs in different stages that include redox reactions and void formation followed by strain field relaxation via formation of defects. This study highlights the relevance of understanding the local dynamics responsible for changes in the particle composition in order to control stability and, ultimately, macroscopic functionality.