Abstract The solid electrolyte interphase (SEI) is an electronically insulating film formed from the decomposition of the organic electrolyte at the surface of the negative electrodes in Li‐ion batteries (LIBs). This film is of vital importance in the performance and safety of LIBs. Atomic force microscopy (AFM) and scanning electrochemical microscopy (SECM) are combined in one platform for the consecutive in situ investigation of surface reactions in LIBs inside an Ar‐filled glovebox. As proof of concept, the formation and the electrochemical properties of the SEI formed on glassy carbon electrodes are investigated. Changes in topography during film formation of the SEI are studied via AFM. The AFM tip is then used to partially remove a small area (50×50 μm 2 ) of the SEI, which is subsequently probed using SECM in feedback mode. The AFM‐scratched spot is clearly visualized in the SECM image, demonstrating the strength of the AFM/SECM combination for the investigation in the field of LIBs.