The aim was to analyze the impact of the intraoral environment on dental biofilm, corrosion of nickel-titanium (NiTi) alloy and the effect of its changed mechanical properties on tooth movement. A randomized controlled trial included 64 subjects aged 12-22 years (57% women) in three groups: (I) group that used the antiseptic chlorhexidine digluconate (CHX) for a period of one month, (II) group that used a gel with a high concentration of fluoride over period of one month, and (III) the control group performing standard oral hygiene. NiTi archwires (dimensions 0.508×0.508mm) were analyzed after three months intraoral exposure and compared to the unexposed NiTi (corrosion behavior, hardness, surface characteristics, friction and elastic properties). The change in the shape of dental arches were measured. The effectiveness of dental biofilm control was assessed. An analysis of changes in the ratio of target bacteria in the dental biofilm was performed by polymerase chain reaction. Exposure to intraoral conditions reduced stifness, flexibility, resilience and hardness of NiTi (p≤0.015). CHX and fluoride did not change these properties more than saliva with regular hygiene. Roughness and friction were not significantly influenced by oral exposure. General corrosion was predominant finding regardless of the additional prophylactic agent. The amount of change in the shape of the dental arch in the maxilla and mandible did not differ significantly between the experimental groups. The fixed metal orthodontic appliance with standard hygiene increased the accumulation and pH of biofilm and the number of white spot lesions of enamel, but it did not increase the extent of gingivitis. Fluorides and CHX during one-month of use did not significantly affect the aforementioned. Metal appliance with standard hygiene increased the number of biofilm bacteria, most Streptoccocus mutans (14.2x) and S. salivarius (3.3x), moderately Veillonella parvula (3x) while least S. sobrinus (2.3x) and Agregatibacter actinomycetemcomitans (1.9x). The use of CHX reduced S. sobrinus (2.2x) and A. actinomycetemcomitans (1.9x). Fluoride reduced A. actinomycetemcomitans (1.3x) and S. sobrinus (1.2x). S. mutans was better controlled by fluorides than with CHX. One-month use of fluorides and CHX does not increase corrosion more than saliva with standard oral hygiene, does not modify the mechanical properties of NiTi and would have no clinical implications in changing orthodontic biomechanics. The metal orthodontic appliance increases the number of dental biofilm bacteria, more cariogenic than periopathogens. Fluoride was best at controlling S. mutans, while CHX was better at controlling S. sobrinus and A. actinomycetemcomitans.