Background: Dental caries is a multifactorial disease that results from interactions of susceptible host, cariogenic microorganisms, and fermentable carbohydrate sources. Our study explored oral microbiome shifts in children before and after dental treatment. Methods: Initial saliva samples were collected from caries free, moderate caries, and severe caries children based on the decayed, missing, and filled teeth index (DMFT/dmft) index. After three months of dental treatment, second saliva samples were gathered from the moderate and severe caries groups. The microbiota was analyzed by 16S rRNA gene-based high-throughput sequencing. Results: Most children with caries were between seven and eight years of age (40%), from middle-income group families (61%), highly educated parents (18% secondary level and 75% tertiary level) with good oral hygiene practices. There was a significant increase in alpha-diversity post-dental intervention. Firmicutes, Bacteroidota, and Proteobacteria were abundant across all samples. Post-treatment, Actinobacteria, and Firmicutes significantly decreased (p < 0.05) while Fusobacteria, Proteobacteria, Spirochaetota, and Synergistota significantly increased (p < 0.05). At genus level, a decreased trend was seen in Streptococcus, Prevotella_7, and Rothia and an increased trend was seen in Fusobacterium, Neisseria, Haemophilus, and Leptotrichia, but was not statistically significant. Conclusions: This study on Malaysian children highlights that dental caries are influenced by factors like age, socioeconomic status, and diet, with oral microbiome diversity increasing post-treatment, though some harmful bacteria persist, indicating a need for targeted oral health education and further research on probiotics’ role in caries prevention.