Silicon is a promising negative electrode for secondary lithium-based batteries, but the electrochemical reversibility of particularly nanostructured silicon electrodes drastically depends on their interfacial characteristics, commonly known as the solid electrolyte interface (SEI). The beneficial origin of certain electrolyte additives or different binders is still discussed controversially owing to the challenging peculiarities of interfacial post-mortem investigations of electrodes. In this work, we address the common difficulties of SEI investigations of porous silicon/carbon nanostructures and study the addition of a fluoroethylene carbonate (FEC) as a stabilizing additive as well as the use of two different binders, carboxymethyl cellulose/styrene-butadiene rubber (CMC/SBR) and polyacrylic acid (PAA), for the SEI formation. The electrode is composed of silicon nanocrystallites below 5 nm diameter allowing a detailed investigation of interfacial characteristics of silicon owing to the high surface area. We first performed galvanostatic long-term cycling (400 times) and carried out comprehensive ex situ characterization of the cycled nanocrystalline silicon electrodes with XRD, EDXS, TEM and XPS. We modified the preparation of the electrode for post-mortem characterization to distinguish between electrolyte components and the actual SEI. The impact of the FEC additive and two different binders on the interfacial layer is studied and the occurrence of diverse compounds, in particular LiF, Li2O and phosphates, is discussed. These results help to understand general issues in SEI formation and to pave the way for the development of advanced electrolytes allowing for a long-term performance of nanostructured Si-based electrodes.