Photoluminescence spectroscopy and atom probe tomography were used to explore the optical activity and microstructure of Er3+-doped Si-rich SiO2 thin films fabricated by radio-frequency magnetron sputtering. The effect of post-fabrication annealing treatment on the properties of the films was investigated. The evolution of the nanoscale structure upon an annealing treatment was found to control the interrelation between the radiative recombination of the carriers via Si clusters and via 4f shell transitions in Er3+ ions. The most efficient 1.53-μm Er3+ photoluminescence was observed from the films submitted to low-temperature treatment ranging from 600°C to 900°C. An annealing treatment at 1,100°C, used often to form Si nanocrystallites, favors an intense emission in visible spectral range with the maximum peak at about 740 nm. Along with this, a drastic decrease of 1.53-μm Er3+ photoluminescence emission was detected. The atom probe results demonstrated that the clustering of Er3+ ions upon such high-temperature annealing treatment was the main reason. The diffusion parameters of Si and Er3+ ions as well as a chemical composition of different clusters were also obtained. The films annealed at 1,100°C contain pure spherical Si nanocrystallites, ErSi3O6 clusters, and free Er3+ ions embedded in SiO2 host. The mean size and the density of Si nanocrystallites were found to be 1.3± 0.3 nm and (3.1± 0.2)×1018 Si nanocrystallites·cm−3, respectively. The density of ErSi3O6 clusters was estimated to be (2.0± 0.2)×1018 clusters·cm−3, keeping about 30% of the total Er3+ amount. These Er-rich clusters had a mean radius of about 1.5 nm and demonstrated preferable formation in the vicinity of Si nanocrystallites.