This research aimed to take a next step towards unravelling the CAP inactivation mechanism for mature (Listeria monocytogenes (Gram positive) and Salmonella Typhimurium (Gram negative)) model biofilms, which will support the further optimization this novel technology. More specifically, we examined how the inactivation mechanism was influenced by the applied processing conditions, i.e., by the electrode configuration, the composition of the gas flow, and the power of the discharge. For each combination of plasma characteristics, we examined if the applied CAP treatment had an effect on (i) the cell membrane, (ii) the intracellular DNA, and (iii) the EPS matrix. In addition, we assessed which (reactive) CAP species were responsible for this lethal/damaging effect and whether these species were able to diffuse into the deeper layers of the biofilms. The results indicated that the inactivation mechanism was indeed influenced by the applied processing conditions. Nevertheless, the bactericidal effect of CAP was always a combination of both damage to the membrane and the DNA, caused by (i) the generation of (intracellular) ROS and RNS, (ii) a drop in pH, and/or (iii) the potential generation of a small amount of UV photons. Moreover, the plasma species were able to penetrate into the deeper layers of the model biofilms and some treatment conditions resulted in an increased biofilm porosity.