Cold atmospheric plasma (CAP) has antimicrobial properties and is also known to stimulate the immune system. These properties could be useful for the development of a novel therapeutic or preventive strategy against respiratory infections in the upper respiratory tract (URT) such as ventilator-associated pneumonia (VAP) without inducing an immune overreaction. This study investigated the cellular responses of polymorphonuclear neutrophils (PMNs) after exposure to CAP in a three-dimensional (3D) model of the URT. In vitro experiments were conducted using PMNs isolated from human blood to assess cell migration, intracellular production of reactive oxygen species (ROS), NETosis, surface marker expression (CD11b, CD62L, and CD66b), and cell death with live cell imaging and flow cytometry. CAP was applied for 5 min using two distinct modalities: pressurized air plasma with a plasma intensive care (PIC) device and nebulized air plasma (NP) with a new humidity resistent surface microdischarge (SMD) plasma source, both developed by Terraplasma Medical GmbH. There were no significant signs of cell damage or overstimulation with either device under the conditions tested. However, the NP device caused milder effects on PMN functionality compared to the PIC device, but also demonstrated reduced antibacterial efficacy and reactive oxygen/nitrogen species (RONS) production, as analyzed with colorimetric/fluorimetric assay kits. These findings highlight a trade-off between the two CAP modalities, each with distinct advantages and limitations. Further studies are necessary to investigate these effects in the clinical setting and evaluate the long-term safety and efficacy of CAP treatment in the URT.