Background: The progression of periodontitis, induced by polymicrobial dysbiosis, can be modified by systemic or environmental factors such as stress or anxiety affecting host response. The purpose of this study is to evaluate the potential associations between psychosocial factors scores or salivary cortisol levels with clinical periodontal parameters and bacterial environment in patients with periodontitis; (2) Methods: Subgingival microbiota was collected in two pathological and one healthy sites from thirty diseased patients (before/after scaling and root planing (SRP)) and from one healthy site from thirty control patients. Usual clinical periodontal parameters were recorded, and a saliva sample was harvested. Patients completed stress and anxiety self-assessment questionnaires. Cortisol concentrations were determined by ELISA and bacteria were identified by PCR; (3) Results: No correlation between salivary cortisol and the stress-anxiety self-declared was found (p > 0.05), but high concentrations of this molecule were associated positively and linearly with periodontal pocket depth (p = 0.04). It appeared that certain psychosocial stressors are associated with a modulation of the bacterial colonization of pockets of diseased group (before/after SRP), notably concerning Tannerella forsythia (p = 0.02), Porphyromonas gingivalis (p = 0.03), Fusobacterium nucleatum (p = 0.049) and Campylobacter rectus (p = 0.01). (4) Conclusion: This study reveals associations between bacteria colonization and psychosocial parameters in periodontitis that needs to be further investigated.