The role of the gut-brain axis is crucial in maintaining homeostasis and regulating neural, hormonal, and immunological activity. This study aimed to evaluate the effects of prebiotic or synbiotic on serum markers related to emotional disorders in individuals with morbid obesity in a triple-blind randomized trial. The sample consisted of 22 subjects, 16 women and 6 men, with a mean age of 41.8 ± 8.5 years and a mean BMI of 47.7 ± 6.8 kg/m2. Serum BDNF concentrations decreased significantly after 30 days of prebiotic supplementation (p=0.017), and when analyzing the difference between the evaluated moments, only this group showed a reduction in this parameter. Serum cortisol concentrations were increased in all groups between the moments evaluated, being statistically significant in the synbiotic supplemented group (p=0.028). Serum TNF-α concentrations increased significantly after 30 days of prebiotic supplementation when compared to the baseline of the group itself (p=0.035): however, this variation did not promote significant difference between the groups evaluated after 30 days of supplementation. The results suggest that low grade chronic inflammatory state may be related to neuroendocrine changes present in emotional disorders, but studies with greater sampling power and correlations with clinical findings are necessary to strengthen this evidence.