Oral diseases represent a significant global health and economic burden, necessitating the development of effective diagnostic tools. This study investigates the volatile organic compound (VOC) profiles of bacteria associated with dental caries and periodontal disease to explore their potential as diagnostic biomarkers. Four microbial strains—Streptococcus mutans (700610), Streptococcus sanguis (NCO 2863), Porphyromonas gingivalis (ATCC 33277), and Fusobacterium nucleatum (PK1594)—were cultured (N = 24), alongside intraoral samples (N = 60), from individuals with common oral diseases. Headspace VOCs were analyzed using gas chromatography-mass spectrometry (GC-MS), and statistical analyses were conducted by applying non-parametric Wilcoxon and Kruskal–Wallis tests. VOC identification was performed using the NIST14 database. Strain-specific VOC signatures were identified, with P. gingivalis and F. nucleatum exhibiting distinct profiles from each other and from Streptococcus strains. Comparative analysis of disease cohorts revealed statistically significant differences at multiple retention times between caries, gingivitis, and periodontitis. These findings suggest that VOC profiling enables differentiation between bacterial strains and disease phenotypes, supporting their potential application as diagnostic biomarkers for oral diseases. This study establishes a foundational framework for VOC-based diagnostic methodologies in dental pathology.