Scaling and root planing remain inadequate in periodontitis treatment caused by dysbiotic microbial dental plaque. The aim of this clinical trial is to evaluate the effects of probiotics and kefir consumption in initial periodontal therapy (IPT) on oral microbiota composition and treatment outcomes in patients with periodontitis. The study was carried out in the Gazi University Department of Periodontology, including a sample size of 36 individuals and utilizing a randomized controlled design. Thirty-six patients with periodontitis were randomly allocated to three groups: one receiving probiotic treatment, another receiving kefir, and a third serving as the control group. Obtaining subgingival microbial samples, we recorded plaque, gingival index, bleeding on probing, periodontal pocket depth, and clinical attachment level (periodontal clinical indices) and then performed IPT. For 14 days, patients took either probiotics, kefir, or no supplements. Data for the first and third months were collected using periodontal clinical indices. DNA sequencing was performed to detect Tannerella forsythia, Porphyromonas gingivalis, and Treponema denticola in subgingival plaque samples collected at baseline and three months. Significant differences were observed regarding periodontal clinical indices among groups in the intragroup comparisons. Moreover, levels of Tannerella forsythia were significantly decreased in all groups. Kefir can be administered in addition to IPT, providing results similar to those observed with probiotics.