We aimed to evaluate the antimicrobial efficacy of photodynamic therapy (PDT) and light-activated disinfection (LAD) on zirconia dental implants contaminated with three bacterial species and investigate if the PDT and LAD cause implant surface alterations. Seventy-two zirconia dental implants were contaminated with a bacterial suspension of Prevotella intermedia, Actinomyces actinomycetemcomitans, and Porphyromonas gingivalis. The implants were subsequently randomly divided into four groups (n = 12 dental implants/each) according to the decontamination protocol: Group 1 (PDT1) - PDT (660 nm, 100 mW) with toluidine blue; Group 2 (PDT2) - PDT (660 nm, 100 mW) with phenothiazine chloride dye; Group 3 (LAD) - light emitting diode (LED) with toluidine blue; and Group 4 (TB) - toluidine blue without the application of light. Implants in the positive control (PC) group were treated with a 0.2% chlorhexidine-based solution, and implants assigned to the negative control (NC) group did not undergo any treatment. Each implant was then placed in tubes containing phosphate buffered saline (PBS) and vortexed for 60 s to remove the remaining bacteria from the implant surface. After 10-fold serial dilutions, 30 μl of the suspension was plated on Brucella agar plates. After 72 h, the colony forming units (CFU) were counted. Distinctive colonies were confirmed with MALDI Biotyper. The implants were analyzed using scanning electron microscope (SEM) to evaluate the possible surface alterations due to PDT or LAD. All study groups had significant reductions in the number of CFUs compared with the NC (p < 0.05). PDT1, the PDT2, and the LAD groups had the largest bacterial reduction with respect to each bacterial species separately and the total bacterial count, and they were more efficient compared with the TB group (p < 0.05). SEM analysis did not reveal any alterations of the implant surface after the treatment procedures. Both PDT protocols and LAD showed high and equal effectiveness in decontamination of zirconia dental implants.