Peri-implant disease is usually caused by the accumulation of dental biofilm around the implant, and this biofilm can irradiate the gingiva tissue, which leads to inflammation and, more severely, to a deterioration of the bone structure. There is a concern regarding the removal of biofilm from the implant surface by using different hygiene instruments. Some hygiene instruments may have some effect on the dental implant surface, resulting in roughening or damage to the implant surfaces. This study reviewed the effects of titanium implant surfaces on different hygiene instruments. A literature search was conducted from PubMed, ScienceDirect, and Scopus databases for articles published from 1992 to 2021. A total of 19 full-text papers with keywords of interest that met all the eligibility criteria were selected. Surface roughness was evaluated with a scanning electron microscope and also using a profilometer, laser scanning, scanning probe, and atomic force microscopes. A metal curette produced a roughened surface on the titanium implant, but a plastic curette did not alter the surface. Instrumentation with rubber cups left the surface unchanged and appeared to smoothen the surface, whereas the air-powder abrasive instrumentation altered the surface with the presence of micro pits and pores. A conventional metal ultrasonic scaler showed significant surface topographical changes and scratches on both titanium surfaces, as a diode laser, light-emitting diode (LED), and laser treatment did not show any alteration on the rough and smooth titanium surfaces. Thus, a non-metallic instrument such as a plastic curette, rubber cups, and novel technology including diode laser, LED, and laser treatment is appropriate and can be used for debridement on smooth and machined titanium implant surfaces as well as sandblasted and acid-etched (SLA), titanium plasma-sprayed (TPS), and resorbable blasted media (RBM) surfaces. The use of metallic instruments should be avoided, and it is not recommended.