Bacteria embedded within biofilms present a challenge to surface decontamination by conventional means. Atmospheric pressure non-thermal plasma processes have emerged as a promising approach to overcoming this problem. We used atmospheric pressure non-equilibrium plasmas (APNPs) to assess planktonic versus biofilm-resident bacterial (Neisseria gonorrhoeae) susceptibility to treatment. The decontamination efficiency of the process was evaluated against bacteria embedded within a biofilm, as well as planktonic cells placed on a glass surface. Bacterial survival was assessed using a combination of colony forming unit (CFU) ability and vital staining with a combination of SYTO9 plus propidium iodide. Both methods revealed an increased resistance of biofilm-resident bacteria compared with planktonic cells, after a 20-min exposure to the APNPs. Transmission electron microscopy revealed disruption and damage to the cell wall, resulting in the release of cytoplasmic compounds, alterations in morphology, and a decrease in cell volume, indicating that APNPs may affect the cell wall. Present results show that biofilm-resident bacteria demonstrate augmented survival when exposed to APNP treatment and therefore that decontamination procedures should take into account this survival when evaluating surface decontamination measures.