We report on structural properties and charge trapping in [(Ge+ SiO2)/SiO2]× 2 films deposited by magnetron sputtering on a periodically corrugated-rippled substrate and annealed in vacuum and forming gas. The rippled substrate caused a self-ordered growth of Ge quantum dots, while annealing in different environments enabled us to separate charge trapping in quantum dots from the trapping at the dot-matrix and matrix-substrate interfaces. We show that the charge trapping occurs mainly in Ge quantum dots in the films annealed in the forming gas, while Si–SiO2 interface trapping is dominant for the vacuum annealed films.