In this study, three plasma treatments on biofilm forms of Halomonas caseinilytica (an extremophile organism) i.e., direct and remote non-thermal atmospheric pressure plasma (NTAPP), and plasma-treated water (PTW) were investigated. In contrast to the direct and the remote NTAPP methods, the distilled water (DW) was separately treated with the direct NTAPP, and then, the PTW was applied to the biofilm forms of H. caseinilytica. This indirect treatment method was compared to direct and remote NTAPP treatments. NTAPPs were also applied to the planktonic forms of H. caseinilytica. The petri dishes exposed both directly and remotely to NTAPPs displayed considerable inhibition zones for bacteria, indicating the plasma’s bactericidal effectiveness against planktonic H. caseinilytica. We found that the direct NTAPP exposure resulted in a four-log reduction in CFU count after 15 s of treatment (complete inactivation time was 180 s) while remote NTAPP exposure resulted in a slightly larger than a two-log reduction in CFU count after 15 s of treatment (complete inactivation time was 300 s), against H. caseinilytica biofilms. When the H. caseinilytica biofilms were suspended in PTW, it took 300 s to achieve complete inactivation. Scanning Electron Microscopy (SEM) was used to investigate changes in the structure of the H. caseinilytica biofilms treated with direct and remote NTAPPs, and PTW.