The goal of the present investigation was to examine effects of a cognitive-behavioral group intervention for pregnant women with subclinically elevated stress, anxiety and/or depression on perceived stress and salivary cortisol levels. Expectant mothers were recruited in gynaecologist practices. They participated in a screening, a standardized diagnostic interview (Munich-Composite Diagnostic Interview, M-CIDI), and were randomly assigned to an intervention (N = 21) and treatment as usual control group (N = 40). The intervention consisted of a manualized cognitive-behavioral group program for expectant mothers with subclinically elevated stress, depression, and/or anxiety symptoms. Stress questionnaire (prenatal distress (PDQ), perceived stress (PSS)) as well as diurnal salivary cortisol assessment took place at T1 (antenatal, preintervention), at T2 (antenatal, post-intervention) and T3 (3-month postpartum). Subjects that participated in the intervention exhibited a significant post-treatment change in morning cortisol (cortisol awakening response, CAR) in contrast to control subjects, F(8,51) = 2.300, p = 0.047. Intervention participants showed a smaller CAR subsequent to the intervention, displaying a lessened stress reaction. This effect was not observed in the control group. In contrast, we failed in discovering a significant difference between the research groups regarding the cortisol area under curve parameter (AUC) and the applied subjective stress questionnaires. Evaluation results were thus heterogeneous. Nevertheless, intervention effects on the CAR are promising. Our results suggest that a cognitive-behavioral intervention might lead to an improvement in the biological stress response of pregnant women with subclinically elevated stress, anxiety, or depressive symptoms.