Removable orthodontic appliances (ROAs) are popular devices to move or retain teeth during or after orthodontic treatments providing a good environment for adhesion and colonization of pathogenic and non-pathogenic organisms. The aim of the present study was to explore the presence and variability of oral PH, levels of Candida Albicans, Candida Dubliniensis, and Streptococcus (S.Mutans) in children before and during the treatment with ROAs. In this clinical trial study, a total of 160 patients aged 8–12 years old in both genders were enrolled from a larger sample of patients who were clinically confirmed to obtain ROAs. They were randomly divided into three groups; 1- PH Group (n=51), 2- Candida Group (n=51), and 3- S.Mutans Group (n=58). Patients were assessed prior (T0) and again one month later (T1) following appliance insertion. The oral cavity was sampled for PH level, Candida species and bacterial species by culture. Paired t-Test and ANOVA were applied for statistical analysis. The level of significance was assumed to be P ≤ 0.05 for all tests. In Group 1, PH values decreased from 6.89±0.5 in T0 to 6.55±0.7 in T1 (0.5% decrease) with statistically significant difference (P=0.002). In group 2, total Candida count at dorsal tongue was more than hard palate. Also, the difference (5.1±6 increase) was significant between the mean Candida count in T0 and T1 (P=0.001). Although the C.Albicans count was more than C.Dubliniensis, the difference was not significant. In group 3, S.mutans showed a significant difference between the two subgroups of case and control (P<0.005). ROAs change the balance to decrease the values as well as increase the proliferation/colonization of Candida specimen and S.mutans. This implicated the importance of paying special attention to oral hygiene in orthodontic patients to prevent oral disease and the aggravation of systemic disease in immunocompromised conditions.