OBJECTIVE: Stunting is a condition of impaired growth in children resulting from chronic malnutrition, characterized by shorter stature compared to peers of the same age. This condition leads to salivary gland dysfunction, which triggers oral dysbiosis and increases the risk of periodontal disease in children. Scaling and root planing (SRP) is the gold standard treatment for periodontal disease, aimed at reducing pathogenic bacterial populations. This study aimed to evaluate the effect of SRP treatment on the oral microbiome profile in the saliva of stunted children. A pre- and post-test study design was employed, involving 10 elementary school children divided into two groups: normal children and stunted children. Each participant underwent scaling, with saliva samples collected before and after the procedure. The oral microbiome profile was analyzed using next-generation sequencing, generating taxonomic data at the phylum, genus, and species level. RESULT: Statistical analysis revealed significant changes in the gingival index, a clinical parameter, in the normal group but not in the stunted group. Scaling resulted in shifts in the microbiome profile in both groups, with the dominant phyla identified as Proteobacteria, Bacteroidota, and Firmicutes. Scaling procedure alters the oral microbiome profile in stunted children without affecting the clinical parameter.