Hybrid carbon nanotube-silicon (CNT–Si) junctions have been investigated by angle resolved photoemission spectroscopy (AR-XPS) with the aim to clarify the effects of a nonstoichiometric silicon oxide buried interface on the overall cell efficiency. A complex silicon oxide interface has been clearly identified and its origin and role in the heterojunction have been probed by exposing the cells to hydrofluoric (HF) and nitric (HNO3) acid. Real-time monitoring of the cell efficiencies during the steps following acid exposure (up to 1 week after etching) revealed a correlation between the thickness and chemical state of the oxide layer and the cell efficiencies. By matching the AR-XPS and Raman spectroscopy with the electrical response data it has been possible to discriminate the effects on the cell efficiency of the buried SiOx interface from those related to CNT acid doping. The overall cell behavior recorded for different thicknesses of the SiOx interface indicates that the buried oxide layer is likely acting as a passivating/inversion layer in a metal–insulator-semiconductor junction.