The development of non-invasive process diagnostic techniques for the control of atmospheric plasmas is a critical issue for the wider adoption of this technology. This paper evaluates the use of a frequency-domain deconvolution of an electro-acoustic emission as a means to monitor and control the plasma formed using an atmospheric pressure plasma jet (APPJ) system. The air plasma system investigated was formed using a PlasmaTreat™ OpenAir applicator. Change was observed in the electro-acoustic signal with changes in substrate type (ceramic, steel, polymer). APPJ nozzle to substrate distance and substrate feature size were monitored. The decoding of the electro-acoustic emission yields three subdatasets that are described by three separate emission mechanisms. The three emissions are associated with the power supply fundamental drive frequency and its harmonics, the APPJ nozzle longitudinal mode acoustic emission and its odd overtones, and the acoustic surface reflection that is produced by the impedance mismatch between the discharge and the surface. Incorporating this knowledge into a LabVIEW program facilitated the continuous deconvolution of the electro-acoustic data. This enabled the use of specific frequency band test limits to control the APPJ treatment process which is sensitive to both plasma processing conditions and substrate type and features.