Plasma-based ambient desorption/ionization sources are versatile in that they enable direct ionization of gaseous samples as well as desorption/ionization of analytes from liquid and solid samples. However, ionization matrix effects, caused by competitive ionization processes, can worsen sensitivity or even inhibit detection all together. The present study is focused on expanding the analytical capabilities of the flowing atmospheric-pressure afterglow (FAPA) source by exploring additional types of ionization chemistry. Specifically, it was found that the abundance and type of reagent ions produced by the FAPA source and, thus, the corresponding ionization pathways of analytes, can be altered by changing the source working conditions. High abundance of proton-transfer reagent ions was observed with relatively high gas flow rates and low discharge currents. Conversely, charge-transfer reagent species were most abundant at low gas flows and high discharge currents. A rather nonpolar model analyte, biphenyl, was found to significantly change ionization pathway based on source operating parameters. Different analyte ions (e.g., MH(+) via proton-transfer and M(+.) via charge-transfer) were formed under unique operating parameters demonstrating two different operating regimes. These tunable ionization modes of the FAPA were used to enable or enhance detection of analytes which traditionally exhibit low-sensitivity in plasma-based ADI-MS analyses. In one example, 2,2'-dichloroquaterphenyl was detected under charge-transfer FAPA conditions, which were difficult or impossible to detect with proton-transfer FAPA or direct analysis in real-time (DART). Overall, this unique mode of operation increases the number and range of detectable analytes and has the potential to lessen ionization matrix effects in ADI-MS analyses.