Semiconducting nanomaterials synthesized using wet chemical techniques play an important role in emerging optoelectronic and photonic technologies. Controlling the surface chemistry of the nano building blocks and their interfaces with ligands is one of the outstanding challenges for the rational design of these systems. We present an integrated theoretical and experimental approach to characterize, at the atomistic level, buried interfaces in solids of InAs nanoparticles capped with Sn2S64- ligands. These prototypical nanocomposites are known for their promising transport properties and unusual negative photoconductivity. We found that inorganic ligands dissociate on InAs to form a surface passivation layer. A nanocomposite with unique electronic and transport properties is formed, that exhibits type II heterojunctions favourable for exciton dissociation. We identified how the matrix density, sulfur content and specific defects may be designed to attain desirable electronic and transport properties, and we explain the origin of the measured negative photoconductivity of the nanocrystalline solids.