Alterations in many metabolites and biochemical pathways have been described in Parkinson’s Disease (PD). However, only a small fraction of these have been replicated in independent studies. As almost every PD patient is treated with dopaminergic medication, it is challenging to discriminate between disease- and drug-related effects, especially in relation to dopamine metabolism. We conducted a large-scale metabolomic study in plasma from 140 idiopathic (IPD), 19PRKN/PINK1-linked PD patients, and 64 healthy controls to disentangle disease-related metabolite alterations from drug-related effects. We distinguished between L-Dopa and non-L-Dopa treated PD patients to uncover nuanced metabolic changes associated with different therapies. We demonstrate that L-Dopa treatment uniquely influences the metabolome, with methyldopa and methoxytyramine, both L-Dopa breakdown products, elevated in L-Dopa-treated IPD andPRKN/PINK-linked PD patients. These alterations were not seen in untreated IPD patients and those on agonist treatment only. Polyamine metabolism alterations, notably elevation of putrescine and ornithine, were partly caused by L-Dopa treatment but also found in non-L-Dopa treated PD patients. In non-L-Dopa-treated patients, endocannabinoid metabolites were lowered and associated with disease duration. We observed lipid metabolism alterations, highlighting potential crosslinks with alpha-synuclein and providing insights into pathophysiological mechanisms. AllPRKN/PINK1-linked PD patients received L-Dopa treatment. However, our data potentially support the well-established role of oxidative damage in these subtypes of PD. In conclusion, our study emphasizes the significant impact of L-Dopa treatment on the metabolome, which might be of relevance not only for metabolomics studies but also for PD biomarker research in general. Finally, our study highlights potential biomarkers and pathways crucial for the understanding disease mechanisms of PD.