The deposition of manganese ions dissolved from the cathode onto the interface between the solid electrolyte interphase (SEI) and graphite causes severe capacity fading in manganese oxide-based cells. The evolution of the SEI layer containing these Mn compounds and the corresponding instability of the layer are thoroughly investigated by artificially introducing soluble Mn ions into a 1 mol L−1 LiPF6 electrolyte solution. Deposition of dissolved Mn ions induces an oxygen-rich SEI layer that results from increased electrolyte decomposition, accelerating SEI growth. The spatial distribution of Mn shows that dissolved Mn ions diffuse through the porous layer and are deposited mostly at the inorganic layer/graphite interface. The Mn compound deposited on the anode, identified as MnF2, originates from a metathesis reaction between LiF and dissolved Mn ion. It is confirmed that ion-exchange reaction occurs in the inorganic layer, converting SEI species to Mn compounds. Some of the Mn is observed inside the graphite; this may cause surface structural disordering in the graphite, limiting lithium-ion intercalation. The continuous reaction that occurs at the inorganic layer/graphite interfacial regions and the modification of the original SEI layer in the presence of Mn ions are critically related to capacity fade and impedance rise currently plaguing Li-ion cells.