In this paper, we demonstrate a simple and effective method to control the visibility of embedded silicon solar cells in building-integrated photovoltaic (BIPV) windows by surface structure modification and metal-oxide back coating. The surface structure modification by etching the front glass in BIPV modules and the use of a thin niobium pentoxide (Nb2O5) film as a back coating enable the silicon solar cells to be hidden from view without a serious loss in the power efficiency. By employing the etched front glass and Nb2O5 back coating, silicon solar cells embedded in the BIPV module exhibited power conversion efficiency of 15.23% and fill factor of 65.05%. We also investigate the origin of the improved photovoltaic performance of the solar cells in the BIPV modules. The surface modification of the front cover glass of the BIPV windows enhances the light absorption in the solar cells, which results in the improved photovoltaic performance degraded by a metal-oxide back coating. We believe that the proposed surface modification which induces light trapping and anti-reflection into the cover glass of the BIPV modules with a metal-oxide back coating film is a promising and practical solution for the successful integration of BIPV windows with high efficiency and invisibility.