Introduction and Aim: The role of gastrointestinal alterations and changes in microbiota in the pathogenesis of Parkinson's disease (PD) is gaining increasing recognition. This study aimed to investigate the impact of dietary habits and nutritional content on gut metabolomes (calprotectin, short-chain fatty acids, zonulin, and lipopolysaccharides) in individuals diagnosed with PD. Materials: In this cross-sectional case–control study, 89 patients with PD and 58 healthy controls were enrolled. Dietary habits over the past month were evaluated using a Food Frequency Questionnaire (FFQ). Metabolome levels from stool and blood samples were analyzed using Enzyme-Linked ImmunoSorbent Assay (ELISA) and gas chromatography. Data analysis was performed using both parametric and non-parametric tests, as well as Spearman correlation analysis. Results: Calprotectin and lipopolysaccharide (LPS) levels were significantly higher in the stool samples of patients with PD compared to controls, whereas butyric acid and isobutyric acid levels were significantly lower. No significant differences were observed between the groups in terms of zonulin, total short-chain fatty acids (SCFA), or acetic acid levels. Nutritional analysis revealed a negative correlation between the consumption of walnuts, olive oil, and fruit and inflammatory markers (calprotectin, LPS) in the PD group. Discussion: The findings support the presence of intestinal barrier dysfunction and inflammation in PD. A correlation was observed between dietary content and the intestinal metabolome profile. These results suggest that dietary interventions may be a potential strategy for managing PD.