The low photovoltaic efficiency of iron pyrite-based solar cells is often related to the presence of sulfur deficiencies. In this paper surfur-rich iron pyrite nanocrystals (FeS2 NCs) are synthesized by the hot injection method and deposited using layer by layer deposition. Optical absorption measurements show substantial sub-bandgap absorption, which is attributed to a sulfur-rich, thin surface layer. Microwave photoconductance measurements show very little signal of films with the original long ligands, while an approximately 100-fold higher signal is observed for films treated with FeCl2 and 1,2-ethanedithiol (EDT) solutions. In mesoporous hybrid systems of FeS2/SnO2 both sub-band-gap and above-band-gap photons lead to electron injection from FeS2 into the SnO2 conduction band. We explain these findings by proposing that pinning of the Fermi level by the surface layer leads to a downward band bending in the direction of the surface within the FeS2 NC. Hence, photoexcited electrons will first move toward the shell where they relax into empty surface states. As the holes remain behind in the core of the nanocrystals, this results in a charge-separated state with a long lifetime. Interestingly, these surface electrons are able to migrate in the FeS2 NP layer by interparticle tunneling and can still decay by injection into SnO2. Hence, our results indicate that SnO2 is a suitable electron acceptor for FeS2. The long-lived charge-separated electrons and holes could be exploited efficiently in photodetectors.