Several antiseptic agents have been proposed for the treatment of peri-implantitis as a complementary therapeutic strategy in addition to mechanical devices. The aim of this study was to compare six different antiseptics, as well as alternative formulations of the same chemical agent, with respect to their decontamination efficacy and impact on chemical properties of the implant surface. Titanium disks with a micro-rough surface, previously contaminated with Porphyromonas gingivalis and Streptococcus mutans biofilms, were treated for 2 min with different antiseptics (liquid sodium hypochlorite 5.25%, gel sodium hypochlorite 5.25%, liquid chlorhexidine 0.2%, gel chlorhexidine 1%, gel citric acid 40%, and gel orthophosphoric acid 37%) or sterile saline solution (control) and their antibacterial activity as well as their ability to remove biofilm were assessed by viable bacterial count and scanning electron microscopy, respectively. Spectroscopic analysis was also performed on non-contaminated disks after exposure to the antiseptics, in order to detect any change in the elemental composition of the titanium surface. All the antimicrobial formulations examined were effective against P. gingivalis and S. mutans biofilms. SEM analysis revealed however that liquid sodium hypochlorite 5.25% was more effective in dissolving biofilm residues. Spectroscopic analysis detected traces of the antiseptics, probably due to insufficient rinsing of the titanium surfaces. In conclusion, since gel formulations of these antiseptic agents possessed a similar antibacterial activity to the liquid formulations, these may be proposed as alternative treatments given their properties to avoid overflows and increase contact time without significant side effects on the bone.