Background <p>Individuals with special health care needs (SHCN) often struggle with maintaining oral hygiene, which increases their risk for periodontal diseases. However, scientific evidence supporting tailored treatment strategies in this population remains limited. This study aimed to evaluate the short-term effects of periodontal treatment on oral microbial profiles in individuals with different types of disabilities and to identify behavioral factors influencing treatment responsiveness.</p> Methods <p>Forty-seven SHCN patients (intellectual disability, autism spectrum disorder, neurological disorders, and others disabilities) were enrolled and underwent up to three dental visits. Gingival crevicular fluid (GCF) samples were collected longitudinally from two sites per patient and analyzed using multiplex qPCR to quantify 13 representative periodontitis-associated and commensal bacteria. Brushing habits and patient characteristics were recorded using structured questionnaires.</p> Results <p>Among the 39 patients who completed all three visits, red-complex pathobionts such as <i>P. gingivalis</i> and <i>T. denticola</i> significantly decreased after treatment, while commensal species like <i>E. corrodens</i> increased. The overall abundance profile initially contracted but partially rebounded by the third visit. Brushing frequency and independence were strongly associated with improved microbial outcomes. Patients with intellectual disability and autism spectrum disorder showed more favorable responses compared to those with neurological disorders.</p> Conclusion <p>Microbial responses to periodontal treatment in individuals with SHCN vary by disability type and oral hygiene behavior. Regular microbial monitoring through non-invasive GCF sampling could provide valuable guidance for personalized oral health management strategies in this population.</p>