To achieve high performance in perovskite solar cells (PSCs), it is very vital to engineer the recombination and extraction of the hole–electron pairs at the electron transport layer (ETL)/perovskite interface. In this research, the main idea is to improve the photovoltaic performance of the cells by modifying the compact ETL surface (≈50 nm thick) by inserting a <10 nm thick ultra-thin layer (UTL) of metal oxide. For this purpose, all types of single layer and bilayer structured ETLs of TiO2, SnO2 and WO3, i.e., three common metal oxide electron transport materials in PSCs, were fabricated using the reproducible and industry-compatible radio-frequency sputtering method and their function as ETLs was then compared. These ETLs and cells were characterized for structural and electrical properties by FESEM, XRD, Mott–Schottky analysis, UV–Vis spectroscopy and J–V measurements. It was found that a significant increase in cell efficiency is achieved due to more efficient energy band alignment using the bilayer structures of TiO2/WO3-UTL, SnO2/WO3-UTL and TiO2/SnO2-UTL. Conversely, reduced efficiency is observed when using their inverted structures, namely WO3/TiO2-UTL, WO3/SnO2-UTL and SnO2/TiO2-UTL. These results suggest a simple and promising strategy to increase the efficiency of photovoltaic devices.