Aim: This study aims to evaluate the clinical and microbiological changes accompanying the inflammatory process of periodontal tissues during treatment with space maintainers (SMs). Materials and Methods: The children were separated into fixed (Group 1, n = 20) and removable (Group 2, n = 20) appliance groups. A full periodontal examination, including probing pocket depth (PPD), bleeding on probing (BOP), and plaque index (PI), was performed. Anaerobic microorganisms in the crevicular fluid were detected with the culture method. Clinical and microbial evaluations were performed before (T0) applications. as well as at three (T1), and 9 months intervals (T2) after the application of the fixed or removable appliances. Results: The PI, PPD, and BOP scores at the testing sites of both groups increased significantly from before treatment (T0) to the 9 months' time frame (T2) (P < 0.05), The presence of anaerobic bacteria in the subgingival dental plaque increased from T0 (n = 13, 65%) to T1 (n = 16, 80%) in the fixed SM group, but not statistically significant. The same values were obtained in T1 and T2 (n = 16, 80%). Conclusion: Although, the results of this study demonstrate that the application of fixed or removable SM appliances in children induced an increase of clinical periodontal parameters, anaerobic microbiota consisting of Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, and Tannerella forshia were not observed in any of the samples in short-term. Further long-term and comprehensive investigations are necessary.