Charge injection and retention in thin dielectric layers remain critical issues due to the great number of failure mechanisms they inflict. Achieving a better understanding and control of charge injection, trapping and transport phenomena in thin dielectric films is of high priority aiming at increasing lifetime and improving reliability of dielectric parts in electronic and electrical devices. Thermal silica is an excellent dielectric but for many of the current technological developments more flexible processes are required for synthesizing high quality dielectric materials such as amorphous silicon oxynitride layers using plasma methods. In this article, the studied dielectric layers are plasma deposited SiO x N y . Independently on the layer thickness, they are structurally identical: optically transparent, having the same refractive index, equal to the one of thermal silica. Influence of the dielectric film thickness on charging phenomena in such layers is investigated at nanoscale using Kelvin probe force microscopy (KPFM) and conductive atomic force microscopy. The main effect of the dielectric film thickness variation concerns the charge flow in the layer during the charge injection step. According to the SiO x N y layer thickness two distinct trends of the measured surface potential and current are found, thus defining ultrathin (up to 15 nm thickness) and thin (15–150 nm thickness) layers. Nevertheless, analyses of KPFM surface potential measurements associated with results from finite element modeling of the structures show that the dielectric layer thickness has weak influence on the amount of injected charge and on the decay dynamics, meaning that pretty homogeneous layers can be processed. The charge penetration depth in such dielectric layers is evaluated to 10 nm regardless the dielectric thickness.