Orthodontic treatment has become increasingly popular due to its benefits in improving facial and smile aesthetics, self-esteem and the function of the stomatognathic apparatus. However, orthodontic appliances make it more difficult to brush teeth effectively, as they interfere with tooth brushing and facilitate the accumulation of dental plaque (biofilm), which induces a quantitative and qualitative change in the oral microbiota. It can cause several adverse effects, such as gingivitis, periodontitis, white spot lesions (WSL), caries and halitosis, induced by an increase in periodontopathogenic and cariogenic bacteria. Therefore, this article resumes the main findings on the changes in the oral microbiota induced by different orthodontic appliances (removable, fixed and clear aligners) and gives some practical strategies in order to reduce the impact and/or incidence of local dental/periodontal complications.