To investigate whether academic stress changes the salivary microbiota and its relationship with salivary parameters, evaluating the effects on the production of volatile sulfur compounds (VSCs) in healthy women. Fifty-five women who were enrolled in a four-year Dentistry course were assessed for academic stress by the questionnaire Maslach Burnout Inventory—Student Survey and were then classified into ‘Not Stressed’ and ‘Stressed’ groups. Cortisol and alpha-amylase (AA) were measured as physiological stress biomarkers. Oral Chroma™ gas chromatograph was used to measure concentrations of hydrogen sulfide (H2S), methyl mercaptan and dimethyl sulfide. Salivary proteins were evaluated by western blot. Quantitative polymerase chain reaction was used to identify the salivary amounts of halitosis-associated bacteria. The ‘Stressed’ volunteers showed higher levels of H2S, AA, Fusobacterium nucleatum and total bacteria, compared to the ‘Not Stressed’ individuals (p < 0.05; Mann–Whitney test). Salivary proteins showed no differences between groups (p > 0.05; Mann–Whitney test). Academic stress was positively correlated with H2S, total bacteria and F. nucleatum counts, while F. nucleatum was positively correlated with AA. H2S showed positive correlations with AA and Solobacterium moorei (p < 0.05; Spearman correlation). Beta-defensin (BD) presented negative correlations with H2S and S. moorei (p < 0.05; Spearman correlation). Academic stress increased salivary F. nucleatum and total bacteria, as well as AA activity. The protein BD showed important correlations with bacteria and VSC. These changes appeared to be accountable for increased H2S production in the stressed women.