This study evaluated the Nutrition Care Process documentation used by dietitians for obese pediatric patients diagnosed with metabolic syndrome (MetS) and/or non-alcoholic fatty liver disease (NAFLD) and its impact on the achievement of nutritional goals. This retrospective cohort study utilized data retrieved from three tertiary care hospitals in Riyadh. A total of 142 obese pediatric patients aged 8–18 years diagnosed with NAFLD and/or MetS were evaluated. Data on weight, height, blood pressure (BP), lipid profile, and liver enzymes were collected. A validated audit was used to assess the documentation quality. Twenty-seven (46.6%) dietitian notes received a high score, 21 (36.2%) received a medium score, and 10 (17.2%) received a low score. There was no significant effect of dietitian audit scores on nutritional outcomes, however, the change in body mass index from 6 to 12 months follow-up period was inversely correlated with the audit score (r = −0.761, p = 0.007), and alkaline phosphatase was inversely correlated with the audit score (r = −0.819, p = 0.013). In conclusion, there was a clear variation in the quality of dietitians’ documentation and the impact of documentation scores on nutritional outcomes.