Objective The number of patients rehabilitated with dental implants has contributed to increased incidence of peri-implant diseases. Due to complex and difficult treatment, peri-implantitis is a challenge and an efficient clinical protocol is not yet established. Aim of this study was to evaluate the efficacy of two protocols for in vitro decontamination of dental implants surface. Material and Methods Twenty titanium implants (BioHE-Bioconect) were used. Implants were divided into five groups (n = 4). NC group (negative control): sterile implants; PC group (positive control): biofilm contaminated implants; S group: biofilm contaminated implants, brushed with sterile saline; SB group: biofilm contaminated implants, brushed with sterile saline and treated with air-powder abrasive system with sodium bicarbonate (1 minute); and antimicrobial photodynamic therapy (aPDT) group: biofilm contaminated implants, brushed with sterile saline and treated with antimicrobial photodynamic therapy (red laser + toluidine blue O). The implants were contaminated in vitro with subgingival biofilm and distributed in groups PC, S, SB, and aPDT. Each group received the respective decontamination treatment, except groups NC and PC. Then, all implants were placed in tubes containing culture medium for later sowing and counting of colony-forming units (CFUs). Statistical Analysis One-way analysis of variance and Tukey tests were performed, at 5% significance level. Results Significantly fewer CFUs were observed in the aPDT group (19.38 × 105) when compared with groups SB (26.88 × 105), S (47.75 × 105), and PC (59.88 × 105) (p < 0.01). Both the aPDT and SB groups were statistically different from the NC group (p < 0.01). Conclusion Proposed protocols, using air-powder abrasive system with sodium bicarbonate and aPDT, showed to be efficacious in the decontamination of dental implants surface in vitro.