Background: Antimicrobial photodynamic therapy (PDT) has been introduced as a potential option for peri-implantitis treatment. The aim of this study is to evaluate the antimicrobial effect of a novel technique involving a combination of 445 nm diode laser light with 0.1% riboflavin solution (used as a photosensitizing dye) as applied on a bacterial–fungal biofilm formed on implants and to compare the performance of this technique with that of the commonly used combination of 660 nm diode laser with 0.1% methylene blue dye. Methods: An in vitro study was conducted on 80 titanium dental implants contaminated with Staphylococcus aureus (SA) and Candida albicans (CA) species. The implants were randomly divided into four groups: negative control (NC), without surface treatment; positive control (PC), treated with a 0.2% chlorhexidine (CHX)-based solution; PDT1, 660 nm (EasyTip 320 µm, 200 mW, Q power = 100 mW, 124.34 W/cm2, 1240 J/cm2) with a 0.1% methylene blue dye; and PDT2, 445 nm (EasyTip 320 µm, 200 mW, Q power = 100 mW, 100 Hz, 124.34 W/cm2, 1.24 J/cm2) with a 0.1% riboflavin dye. Results: The PDT1 and PDT2 groups showed greater reduction of SA and CA in comparison to the NC group and no significant differences in comparison to the PC group. No statistically significant differences between the PDT1 and PDT2 groups were observed. Conclusions: A novel antimicrobial treatment involving a combination of 445 nm diode laser light with riboflavin solution showed efficiency in reducing SA and CA biofilm formation on dental implant surfaces comparable to those of the more commonly used PDT treatment consisting of 660 nm diode laser light with methylene blue dye or 0.2% CHX treatment.