The investigation of molecular interactions between silica phases and organic components is crucial for elucidating the main steps involved in the biosilica mineralization process. In this respect, the structural characterization of the organic/inorganic interface is particularly useful for a deeper understanding of the dominant mechanisms of biomineralization. In this work, we have investigated the interaction of selectively C-13- and N-15-labeled atoms of organic long-chain polyamines (LCPAs) with Si-29-labeled atoms of a silica layer at the molecular level. In particular, silica/LCPA nanocomposites were analyzed by solid-state NMR spectroscopy in combination with all-atom molecular dynamics simulations. Solid-state NMR experiments allow the determination of Si-29-N-15 and Si-29-C-13 internuclear distances, providing the parameters for direct verification of atomistic simulations. Our results elucidate the relevant molecular conformations as well as the nature of the interaction between the LCPA and a silica substrate. Specifically, distances and second moments suggest a picture compatible with (i) LCPA completely embedded in the silica phase and (ii) the charged amino groups located in close vicinity of silanol groups.