Background: Several studies point to a correlation between obesity and the severity of depressive and anxiety symptoms in children and adults, but there are still some controversial points about this association. The aim of this study is to investigate the relationship between body composition and the severity of anxiety/depressive symptoms in overweight and obese individuals with Metabolic Syndrome (MS). Methods: Fifty patients, 18-50 years old, overweight or obese and with the diagnosis of MS based on the International Diabetes Federation (IDF) criteria were selected for this study. Body composition was evaluated using Dual Energy X-ray Absorptiometry (DXA). Depressive symptoms were evaluated using the Hospital Anxiety and Depression Scale (HADS-Depression) and the Beck Depression Inventory (BDI). Anxiety symptoms were evaluated using HADS-Anxiety. Results: No correlation was found between depressive symptoms (HADS-Depression or BDI) and Body Mass Index (BMI) (r = 0.01; p = 0.94 and r = −0.12, p = 0.38; respectively), Waist Circumference (WC) (r = −0.06, p = 0.67 and r = −0.22, p = 0.12; respectively), and Waist-to-Hip Ratio (WHR) (r = −0.12, p = 0.40 and r = −0.17, p = 0.23; respectively). Additionally, no correlation was found among anxiety symptoms (HADS-Anxiety) and BMI (r = −0.15, p = 0.27), and WHR (r = −0.17, p = 0.24). In contrast, a significant correlation was found between percentage of total fat (DXA) and HADS-Depression (r = 0.34, p = 0.019) and HADS-Anxiety (r = 0.30, p = 0.039). Additionally, an inverse and strong correlation was found between lean mass (in grams) and HADS-Depression (r = −0.42, p = 0.004), HADS anxiety (r = −0.57, p < 0.0001), and BDI (r = −0.44, p = 0.026). Conclusions: In individuals with MS, the percentage of body fat, and not central fat, BMI, WC, or WHR, was associated with an increased severity of anxiety and depressive symptoms. In contrast, total lean mass was strongly associated with fewer anxiety/depressive symptoms, suggesting that body composition might be related to psychiatric comorbidity in overweight individuals with MS.