Parkinson’s disease is (PD) a progressive neurodegenerative disorder. This study investigated the effects of an individualized nutritional intervention based on the Ketoflex 12/3 protocol, in addition to standard medical treatment, on motor and non-motor symptoms in PD.  40 individuals with PD were included in the study, and participants were randomly assigned to intervention and control. All individuals were classified according to inflammatory, glycotoxic, toxic, and vascular biotypes. The intervention group was assigned a plant-rich diet with a low glycemic index, consistent with ketogenic principles, free of inflammatory effects, and including intermittent fasting. The primary endpoint was the change in motor symptoms measured by the Unified Parkinson’s Disease Rating Scale part III (UPDRS-III) from baseline to six months. Secondary endpoints included apathy (Starkstein Apathy Scale), activities of daily living (ADL/IADL), and gastrointestinal function (Bristol stool scale). Compared with the control group, the intervention group showed a significantly greater improvement in motor symptoms as measured by UPDRS-III (−11.0 vs +2.1 points from baseline to six months; p < 0.001). Significant between-group differences were also observed for secondary endpoints, including apathy (Starkstein Apathy Scale), activities of daily living (ADL/IADL), and gastrointestinal function (Bristol stool scale), all favoring the intervention group. Spearman correlation analyses revealed significant negative correlations with ADL and UPDRS-III scores, particularly in individuals with an inflammatory phenotype. The findings suggest an individualized nutritional approach may contribute to improvement in both motor and non-motor symptoms in PD. Larger, multi-center trials with extended follow-up are needed.