A broad interest has been showed recently on the study of nanostructuring of thin films and surfaces obtained by low-energy He plasma treatments and He incorporation via magnetron sputtering. In this paper spatially resolved electron energy-loss spectroscopy in a scanning transmission electron microscope is used to locate and characterize the He state in nanoporous amorphous silicon coatings deposited by magnetron sputtering. A dedicated MATLAB program was developed to quantify the helium density inside individual pores based on the energy position shift or peak intensity of the He K-edge. A good agreement was observed between the high density (~35–60 at nm−3) and pressure (0.3–1.0 GPa) values obtained in nanoscale analysis and the values derived from macroscopic measurements (the composition obtained by proton backscattering spectroscopy coupled to the macroscopic porosity estimated from ellipsometry). This work provides new insights into these novel porous coatings, providing evidence of high-density He located inside the pores and validating the methodology applied here to characterize the formation of pores filled with the helium process gas during deposition. A similar stabilization of condensed He bubbles has been previously demonstrated by high-energy He ion implantation in metals and is newly demonstrated here using a widely employed methodology, magnetron sputtering, for achieving coatings with a high density of homogeneously distributed pores and He storage capacities as high as 21 at%.