This paper presents the results from an experimental study of the ion flux characteristics behind the remote plasma zone in a vertical tube reaction chamber for atmospheric pressure plasma enhanced chemical vapor deposition. Capacitively coupled radio frequency plasma was generated in pure He and gas mixtures: He–Ar, He–O2, He–TEOS. We previously used the reaction system He–TEOS for the synthesis of self-assembled structures of silicon dioxide nanoparticles. It is likely that the electrical parameters of the area, where nanoparticles have been transported from the synthesis zone to the substrate, play a significant role in the self-organization processes both in the vapor phase and on the substrate surface. The results from the spatial distribution of the electrical potential and ion concentration in the discharge downstream area measured by means of the external probe of original design and the special data processing method are demonstrated in this work. Positive and negatives ions with maximum concentrations of 106–107 cm−3 have been found at 10–80 mm distance behind the plasma zone. On the basis of the revealed distributions for different gas mixtures, the physical model of the observed phenomena is proposed. The model illustrates the capability of the virtual ion emitter formation behind the discharge gap and the presence of an extremum of the electrical potential at the distance of approximately 10−2–10−1 mm from the grounded electrode.