While intensive efforts have been devoted to studying the nature of the solid-electrolyte interphase (SEI), little attention has been paid to understanding its role in the mechanical failures of electrodes. Here we unveil the impact of SEI inhomogeneities on early-stage defect formation in Si electrodes. Buried under the SEI, these early-stage defects are inaccessible by most surface-probing techniques. With operando full field diffraction X-ray microscopy, we observe the formation of these defects in real time and connect their origin to a heterogeneous degree of lithiation. This heterogeneous lithiation is further correlated to inhomogeneities in topography and lithium-ion mobility in both the inner- and outer-SEI, thanks to a combination of operando atomic force microscopy, electrochemical strain microscopy and sputter-etched X-ray photoelectron spectroscopy. Our multi-modal study bridges observations across the multi-level interfaces (Si/LixSi/inner-SEI/outer-SEI), thus offering novel insights into the impact of SEI homogeneities on the structural stability of Si-based lithium-ion batteries.