Fluorine-based additives have a tremendously beneficial effect on the performance of lithium-ion batteries, yet the origin of this phenomenon is unclear. This paper shows that the formation of a solid-electrolyte interphase (SEI) on the anode surface in the first five charge/discharge cycles is affected by the stereochemistry of the electrolyte molecules on the anode surface starting at open-circuit potential (OCP). This study shows an anode-specific model system, the reduction of 1,2-diethoxy ethane with lithium bis(trifluoromethane)sulfonimide, as a salt on an amorphous silicon anode, and compares the electrochemical response and SEI formation to its fluorinated version, bis(2,2,2-trifluoroethoxy) ethane (BTFEOE), by sum frequency generation (SFG) vibrational spectroscopy under reaction conditions. The SFG results suggest that the CF3 end-groups of the linear ether BTFEOE change their adsorption orientation on the a-Si surface at OCP, leading to a better protective layer. Supporting evidence from ex situ scanning electron microscopy and X-ray photoelectron spectroscopy depth profiling measurements shows that the fluorinated ether, BTFEOE, yields a smooth SEI on the a-Si surface and enables lithium ions to intercalate deeper into the a-Si bulk.