High resolution scanning transmission electron microscopy with an aberration corrected and monochromated instrument has been used for the assessment of the silicon-based active layer stack for novel optoelectronic devices. This layer contains a multilayer structure consisting of alternate thin layers of pure silica (SiO2) and silicon-rich silicon oxide (SRO, SiOx). Upon high temperature annealing the SRO sublayer segregates into a Si nanocluster (Si-nc) precipitated phase and a SiO2 matrix. Additionally, erbium (Er) ions have been implanted and used as luminescent centres in order to obtain narrow emission at 1.54 μm. Our study exploits the combination of high angle annular dark field (HAADF) imaging with a sub-nanometer electron probe and electron energy loss spectroscopy (EELS) with an energy resolution below 0.2 eV. The structural and chemical information is obtained from the studied multilayer structure. In addition, the instrumental techniques for calibration, deconvolution, fitting and analysis of the EELS spectra are explained in detail. The spatial distribution of the Si-nanoclusters (Si-ncs) and the SiO2 barriers is accurately delimited in the multilayer. Additionally, the quality of the studied multilayer in terms of composition, roughness and defects is analysed and discussed. Er clusterization has not been observed; even so, blue-shifted plasmon and interband transition energies for silica are measured, in the presence of Er ions and sizable nanometer-size effects.