Background The aim of the current study was to comparatively assess the efficiency of three different adjunctive therapy options (cold atmospheric plasma, [CAP], photodynamic therapy [PDT] and chemical decontamination via 35% phosphoric acid gel [PAG]) on decontamination of titanium implant surfaces in-vitro. Materials and methods Implants were inserted in concavities of four mm in depth mimicking a bone defect at the implant recipient site. In each model, two implants were inserted in the fourth and one implant in the third quadrants. After contamination with E. faecalis, the first group has been treated with CAP for 3 min, the second group with 35% PAG (and the third group with PDT. After treatment, quantification of bacterial colonization was assessed by quantification via colony forming units and qualitatively by fluorescence microscopy and scanning electron microscopy. Results With a mean value of 1.24 × 105 CFU/ml, the CAP treated implants have showed the least microorganisms. The highest number of CFU was found after PDT with mean value of 8.28 × 106 CFU/ml. For the implants that were processed with phosphoric acid, a mean value of 3.14 × 106 CFU/ml could be detected. When the groups were compared, only the CAP and PDT groups differed significantly from each other (p = 0.005). Conclusion A complete cleaning of the micro-textured implant surface or the killing of the bacteria could not be achieved by any of the investigated treatment options, thus bacteria in the microstructure of the titanium surface cannot be completely reached by mechanical and physico-chemical processes. Clinical relevance The main goal of the adjunctive peri-implantitis treatment is the decontamination of the implant surface. However, there is still an ongoing need to define the most appropriate adjunctive therapy method. Due to its antimicrobial effects, CAP combined with mechanical debridement could be a feasible treatment modality in the management of peri-implantitis.