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(1) Introduction: Zonulin (ZO) has been proposed as a marker of intestinal permeability. Only a few studies have analyzed to date how diet influences the serum concentration of ZO among patients with non-alcoholic fatty liver disease (NAFLD). We performed a six-month dietetic intervention to evaluate the association between fiber intake and ZO concentration in 32 individuals with NAFLD. (2) Methods: Fiber content in the diet was estimated by Food Frequency Questionnaire (FFQ) and by analyzing 72-h nutritional diaries. ZO concentrations in serum were measured before and after the intervention by immunoenzymatic assay (ELISA). Fatty liver was quantified using the Hamaguchi score before and after the dietetic intervention. (3) Results: During the intervention, the dietary fiber intake increased from 19 g/day to the 29 g/day concomitant with an increase in the frequency of fiber consumption. All patients experienced significant (all p < 0.05) improvements in serum aspartate aminotransferase (AST), alanine aminotransferase (ALT) and gamma-glutamyltransferase (GGTP) activities. We also detected decreased serum triglycerides (p = 0.036), homeostatic model assessment insulin resistance (HOMA-IR (p = 0.041) and insulin content (p = 0.34), and improvement of fatty liver status according to the Hamaguchi score (p = 0.009). ZO concentration in serum decreased by nearly 90% (7.335 ± 13.492 vs. 0.507 ± 0.762 ng/mL, p = 0.001) and correlated with the amount of dietary fiber intake (p = 0.043) as well as the degree of fatty liver (p = 0.037). (4) Conclusion: Increasing nutritional fiber results in reduced serum ZO levels, reduced liver enzymes and …