Nonaqueous solvents in modern battery technologies undergo electroreduction at negative electrodes, leading to the formation of a solid-electrolyte interphase (SEI). The mechanisms and reactions leading to a stable SEI on silicon electrodes in lithium-ion batteries are still poorly understood. This lack of understanding inhibits the rational design of electrolyte additives, active material coatings, and the prediction of Li-ion battery life in general. We prepared SEI with a common nonaqueous solvent (LiPF6 in PC and in EC/DEC 1:1 by wt %) on silicon oxide and etched silicon (001) surfaces in various states of lithiation to understand the role of surface chemistry on the SEI formation mechanism and SEI structure. Anhydrous and anoxic techniques were used to prevent air and moisture contamination of prepared SEI films, allowing for more accurate characterization of SEI chemical stratification and composition by X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (TOF-SIMS) depth profiling. Additionally, multivariate statistical methods were used to better understand TOF-SIMS depth profiling studies. We conclude that the absence of native-oxide layer on silicon has a significant impact on the formation, composition, structure, and thickness of the SEI.