The solid-electrolyte interphase (SEI) dictates the performance of most batteries, but the understanding of its chemistry and structure is limited by the lack of in situ experimental tools. In this work, we present a dynamic picture of the SEI formation in lithium-ion batteries using in operando liquid secondary ion mass spectrometry in combination with molecular dynamics simulations. We find that before any interphasial chemistry occurs (during the initial charging), an electric double layer forms at the electrode/electrolyte interface due to the self-assembly of solvent molecules. The formation of the double layer is directed by Li+ and the electrode surface potential. The structure of this double layer predicts the eventual interphasial chemistry; in particular, the negatively charged electrode surface repels salt anions from the inner layer and results in an inner SEI that is thin, dense and inorganic in nature. It is this dense layer that is responsible for conducting Li+ and insulating electrons, the main functions of the SEI. An electrolyte-permeable and organic-rich outer layer appears after the formation of the inner layer. In the presence of a highly concentrated, fluoride-rich electrolyte, the inner SEI layer has an elevated concentration of LiF due to the presence of anions in the double layer. These real-time nanoscale observations will be helpful in engineering better interphases for future batteries. An operando mass spectrometry technique, along with molecular dynamics simulations, unveils the evolution of the solid-electrolyte interphase chemistry and structure in lithium-ion batteries during the first cycle.