Individuals with dentofacial deformities often display a low quality of life (QoL) through biological mechanisms that remain unraveled. In this case-control study, the salivary levels of cytokines, glutamate, and kynurenine metabolites were assessed in patients undergoing orthognathic surgery (OS), while correlating these parameters with QoL and psychological symptoms. Thirty-six patients were enrolled in control (under orthodontic treatment) and test (undergoing OS) groups, matched by age and sex. The QoL was assessed through the World Health Organization Quality of Life BREF (WHOQOL-BREF) and the Orthognathic Quality of Life Questionnaire (OQLQ). The psychological symptoms were evaluated by the Satisfaction with Life Scale, the Rosenberg Self-Esteem Scale (RSES), and the Depression, Anxiety, and Stress Scale-21 (DASS-21). The salivary levels of IL-1β, IL-6, IL-10, glutamate, and kynurenine metabolites were evaluated. The OQLQ demonstrated increased QoL scores in the test group, regarding social aspects, facial esthetics, and function domains, without significant differences in respect to the other surveys. These patients displayed higher IL-1β and glutamate levels; conversely, the kynurenine metabolites were unaltered. The glutamate levels positively correlated with the OQLQ function scores. The data brings novel evidence about the psychobiological features of patients with dentofacial deformities, showing salivary variations of inflammatory biomarkers in these individuals.