Patients undergoing implant treatment are at risk of peri-implant bone loss, which is most often caused by the adverse effects of microorganisms, but there are few proven procedures for their reduction. The aim of the research was to identify the microorganisms inhabiting the composites used to close the screw access hole (SAH), compare them numerically with those present on the surface of crowns and teeth, and optimize the doses of the diode laser, which will reduce microorganisms and will not deteriorate the roughness of polished composites. Patients were swabbed from the surface of SAH composites, from porcelain and zirconium restorations, and from teeth, and then the number of microorganisms was determined by using a culture technique. Microorganisms were identified by MALDI–TOF MS and NGS sequencing. The effectiveness of diode laser irradiation was achieved by using four variants of exposure. After polishing and laser irradiation, the surface roughness of the composites was studied by using optical profilometry. On the surface of SAH, 106 to 108 microorganisms were identified at 0.4 cm2, including many pathogenic species. Among the materials used for the reconstruction of dental implants, the greatest microbiological contamination was found on the composites used to close the SAH. The diode laser with a wavelength of 810 nm with an average power of 3.84 W, during 60 s and 2 × 30 s, has a biocidal effect and does not significantly change the surface roughness of composites. The best reduction of microorganisms was achieved on a composite polished with a polishing rubber and then with a Sof-Lex™ Pre-Polishing Spiral beige (3M ESPE, Ave. St. Paul., MN, USA). Studies have shown that using the optimal laser dose can help treat periimplantitis. These studies provide important information on the possibility of the effective elimination of microorganisms by using a diode laser in the treatment of peri-implant bone loss.