Objective The aim of our study is to better understand the genetic architecture and pathological mechanisms underlying neurodegeneration in idiopathic Parkinson's disease (iPD). We hypothesized that a fraction of iPD patients may harbor a combination of common variants in nuclear‐encoded mitochondrial genes ultimately resulting in neurodegeneration. Methods We used mitochondria‐specific polygenic risk scores (mitoPRSs) and created pathway‐specific mitoPRSs using genotype data from different iPD case–control datasets worldwide, including the Luxembourg Parkinson's Study (412 iPD patients and 576 healthy controls) and COURAGE‐PD cohorts (7,270 iPD cases and 6,819 healthy controls). Cellular models from individuals stratified according to the most significant mitoPRS were subsequently used to characterize different aspects of mitochondrial function. Results Common variants in genes regulating Oxidative Phosphorylation (OXPHOS‐PRS) were significantly associated with a higher PD risk in independent cohorts (Luxembourg Parkinson's Study odds ratio, OR = 1.311.14–1.50, p‐value = 5.4e‐04; COURAGE‐PD OR = 1.231.18–1.27, p‐value = 1.5e‐29). Functional analyses in fibroblasts and induced pluripotent stem cells‐derived neuronal progenitors revealed significant differences in mitochondrial respiration between iPD patients with high or low OXPHOS‐PRS (p‐values < 0.05). Clinically, iPD patients with high OXPHOS‐PRS have a significantly earlier age at disease onset compared to low‐risk patients (false discovery rate FDR‐adj p‐value = 0.015), similar to prototypic monogenic forms of PD. Finally, iPD patients with high OXPHOS‐PRS responded more effectively to treatment with mitochondrially active ursodeoxycholic acid. Interpretation OXPHOS‐PRS may provide a precision medicine tool to stratify iPD patients into a pathogenic subgroup genetically defined by specific mitochondrial impairment, making these individuals eligible for future intelligent clinical trial designs. ANN NEUROL 2024;96:133–149