The electrical characteristics and deep-level transient spectroscopy of a hybrid poly(3,4-ethylene dioxythiophene):poly(styrenesulfonate) (PEDOT:PSS)/GeNCs/Si heterojunction with Ge nanoclusters grown by molecular beam epitaxy on a p-type Si(001) substrate are investigated. The heterostructure shows good rectifying J–V characteristics, the dark current exhibits an activation energies of 280 meV and 550 meV, while the reverse bias leakage current is suppressed due to the coating of Ge nanoclusters with PEDOT:PSS. We show that recombination via deep hole states close to grain boundaries can be partly suppressed by the PEDOT:PSS thin films, leading to a decrease in the saturation current and an improvement of the rectification without deterioration of forward current.