Plasma-based ambient desorption/ionization (ADI) sources for mass spectrometry (MS) often use helium as the primary discharge gas due to the large reaction cross section of excited helium species with atmospheric gases, which ultimately leads to efficient reagent-ion formation. However, some studies have shown that mixed-gas plasmas provide unique advantages. For instance, our group showed that a helium‑oxygen flowing atmospheric-pressure afterglow (He:O2-FAPA) source yielded enhanced ion signals for small polar analytes, but compounds with aromatic rings underwent chemical modification to produce pyrylium species. Here, it is shown that the addition of H2 to the helium FAPA gas significantly decreased the reagent-ion signals, but analyte-ion signal was not affected to the same degree. In addition, mass spectra obtained with He:H2-FAPA were chemically cleaner with fewer ions stemming from analyte species and produced less oxidation of analytes. Addition of nitrogen increased the abundance of negative reagent ions (e.g., NO2− and NO3−) which led to enhanced ion signal for RDX. To better understand these unique advantages of a mixed-gas FAPA, the impact of molecular-gas (O2, N2, or H2) addition on the optical-emission spectra from the discharge was also measured. Spatially resolved emission was obtained from the anode- and negative-glow regions. In general, addition of small fractions (~0.1%) of molecular gases decreased helium and OH emission intensities. Atomic oxygen and hydrogen emission increased with the addition of O2 and H2, respectively. Furthermore, emission characteristics of N2, N2+, and NO with respect to molecular gas composition on He-FAPA were measured. Fundamental plasma parameters, such as OH rotational temperature (Trot), were also calculated for these mixed-gas systems.