Structural instability due to intercalation-induced stresses in electrode materials is one of the key degradation mechanisms of Li-ion batteries. Fragmentation of material degrades structural integrity and electrical resistance, and also accelerates harmful side reactions. In situ experiments are the appropriate approach for investigating the actual time-dependent nature of the behavior changes of an electrode material while it is charged and discharged. In the current work, a unique in situ electrochemical atomic force microscopy (ECAFM) measurement is made on samples of cylindrical shape, which are micro-machined by focused ion beam (FIB) microscopy. This pre-defined geometry allows the exclusion of secondary, non-active materials from the electrochemically active material as well as the removal of any vagueness owing from the irregular geometry of particles. The experimental results are also used to validate a proposed coupled electrochemical and mechanical model for determining the stress–strain state of active electrode material during electrochemical cycling. The results produced using this model correlate strongly with the experimental data. The combined results reveal the key effects of the geometry, kinetics, and mechanics of electrode materials on the stress–strain state, which acts as a barometer of the structural stability of a material.