Periodontal disease is driven by a dysbiotic subgingival microbiota enriched in anaerobic pathogens, and novel antimicrobial strategies are needed to complement conventional therapy. This pilot study assessed changes in the subgingival microbiota following diode laser-activated indocyanine green-based treatment (EmunDo) using 16S rDNA amplicon sequencing of paired samples collected before and after therapy. Microbiome analysis revealed compositional shifts across all taxonomic levels, with reductions in disease-associated genera including Porphyromonas, Treponema, Fretibacterium, and Prevotella, and relative increases in taxa more commonly associated with periodontal health, such as Streptococcus, Actinomyces, and Haemophilus. Functional prediction further suggested treatment-associated variation in metabolic categories. Overall microbial richness was preserved between groups. These findings suggest that EmunDo treatment was associated with a restructuring of the subgingival microbiota toward a less dysbiotic profile, warranting further investigation in larger controlled studies using higher-resolution approaches such as shotgun metagenomics.