Atmospheric pressure plasma jets (APPJs) can enable large fluxes of reactive species impinging on treated substrates in many applications. The relative importance of ionic versus neutral reactive species fluxes produced by APPJs is to date mainly deduced from modeling due to the challenge of measuring absolute ion densities/fluxes. In this study, a calibration was performed to determine the absolute densities of cold ions in the afterglow region of an radiofrequency-driven APPJ in Ar+ 1% O 2 by molecular beam mass spectrometry. Positive ion densities were found to be about 3–4 orders of magnitudes lower than the densities of the dominant reactive neutral species (O, O 2 (a 1 Δ g), O 3) in the afterglow region of the APPJ at a distance larger than 2 mm from the visible plasma plume. The results illustrate the ability of molecular beam mass spectrometry to enable a quantitative evaluation of both neutral and ionic species in many applications using APPJs.