Mitochondrial disorders are a subset of hereditary diseases characterized by defects in mitochondrial functionality due to mutations in genes in nuclear or mitochondrial DNA. The molecular hallmarks of mitochondrial disorders include a high production of reactive oxygen species (ROS), morphological and functional mitochondrial aberrations, and metabolic impairments. From a systemic perspective, these molecular and cellular impairments can lead to severe disorders affecting the central nervous system, besides to muscles, heart, and gastrointestinal problems. The treatment of mitochondrial diseases with antioxidant moieties like idebenone and resveratrol has been proposed and tested as a potential therapy for these disorders. Polydopamine nanoparticles (PDNPs) are nanostructures derived from the oxidative self-polymerization of dopamine and characterized by high biocompatibility and biodegradability, the ability to be easily functionalized with active molecules, high antioxidant properties, and the ability to act as photothermal conversion agents when irradiated with near infrared (NIR) light. In this work we tested the potential of PDNPs as a non-pharmaceutical treatment for two mitochondrial diseases, namely mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS) and progressive external ophthalmoplegia (PEO). We tested PDNPs on fibroblasts derived from healthy subjects and fibroblasts derived from MELAS and PEO patients. The cells were first characterized from a molecular point of view through proteomic analysis. Then, the biocompatibility, internalization rate, intracellular localization, and protective antioxidant properties of PDNPs were assessed. Lastly, the antioxidant properties of PDNPs were also confirmed on an in vivo model based on zebrafish embryos. Our data demonstrates the ability of PDNPs to protect both healthy and patient-derived cells from ROS-induced damage, thus preventing the increment of oxidative stress, ROS-induced apoptosis, and mitochondrial dysfunctions. Eventually, PDNPs showed the capacity to protect zebrafish embryos from pro-oxidative stimuli. Altogether, this work demonstrates the potential of polydopamine nanostructures as an effective countermeasure for some of the molecular hallmarks associated with mitochondrial disorders, paving the way for the future exploitation in clinical applications.