Orthodontic appliances significantly influence the microbiological dynamics within the oral cavity, transforming symbiotic relationships into dysbiotic states that can lead to periodontal diseases. This review synthesizes current findings on how orthodontic treatments, particularly fixed and removable appliances, foster niches for bacterial accumulation and complicate oral hygiene maintenance. Advanced culture-independent methods were employed to identify shifts toward anaerobic and pathogenic bacteria, with fixed appliances showing a more pronounced impact compared to clear aligners. The study underscores the importance of meticulous oral hygiene practices and routine dental monitoring to manage these microbial shifts effectively. By highlighting the relationship between appliance type, surface characteristics, treatment duration, and microbial changes, this review aims to enhance dental professionals' understanding of periodontal risks associated with orthodontic appliances and strategies to mitigate these risks. The findings are intended to guide clinicians in optimizing orthodontic care to prevent plaque-associated diseases, ensuring better periodontal health outcomes for patients undergoing orthodontic treatment.