Peri-implant diseases can still develop despite oral hygiene practices being maintained. Consequently, regular debridement must be carried out to ensure the implant is sustained. This review evaluated bacterial colonization on implants following the use of different hygiene instruments. A literature search was conducted in PubMed, ScienceDirect, and Scopus databases for articles published from 2012 to 2022. A total of 19 full-text papers were selected. The number of bacteria colonized was most commonly evaluated with a scanning electron microscope (SEM) or by colony-forming unit (CFU) counts, crystal violet assays, plaque index, probing depth, bleeding on probing, turbidity test, and live-dead assays. Rubber cup polishing with an abrasive paste showed a significantly greater reduction in biofilm formation compared with air abrasion with glycine powder, while the air abrasion treatment was found to be more efficient than piezoelectric, carbon, and stainless steel scalers. Surface treatment with Er, Cr: YSGG laser, and Er: YAG laser resulted in statistically significant superior dental biofilm removal compared with titanium curettes and photodynamic therapy. Air abrasion, plastic curette, titanium curette, and ultrasonic scaler showed no significant differences in bacterial colonization, but air abrasion and plastic curette were safer for zirconia implant decontamination. Furthermore, the titanium brush showed better results in decontaminating the implant surface than the Er: YAG laser. Although no single instrument or method could be considered as offering a gold standard in treating peri-implant diseases, the use of air abrasion with glycine powder, laser therapies, rubber cup polishing with an abrasive paste, and a titanium brush had high levels of cleaning efficacy and acceptance by patients.