Many studies have investigated the effects of fixed orthodontic appliances on periodontal health, dental caries, and microbial flora. However, none have examined the impact of different arch wires (Nickel Titanium (NITI) and Stainless Steel (SS)) ligated with elastomeric rings. This study assessed changes in periodontal health, caries development, and bacterial types and counts in 45 patients undergoing orthodontic treatment. The patients were treated with NITI arch wires for three months (Time 1), followed by SS arch wires for three months (Time 2). Clinical measurements (Gingival Index, Plaque Index, pocket depth, and caries development) and microbial changes were recorded at three stages: before bonding (Time 0), Time 1, and Time 2. Treatment with NITI arch wires at Time 1 significantly increased plaque, gingival bleeding, and pocket depth compared to baseline, likely due to NITI's flexibility and surface texture. Switching to SS arch wires at Time 2 resulted in decreased plaque and gingival bleeding due to SS's smoother surface. Despite these changes, caries incidence remained stable. Microbial analysis showed an increase in bacterial colonies from 2,171 at Time 0 to 4,046 at Time 1, dominated by gram-negative bacteria. At Time 2, the colony count decreased to 2,622, but gram-negative bacteria remained prevalent.