Deregulation of mitochondrial network in terminally differentiated cells contributes to a broad spectrum of disorders. Methylmalonic acidemia (MMA) is one of the most common inherited metabolic disorders, due to deficiency of the mitochondrial methylmalonyl-coenzyme A mutase (MMUT). How MMUT deficiency triggers cell damage remains unknown, preventing the development of disease-modifying therapies. Here we combine genetic and pharmacological approaches to demonstrate that MMUT deficiency induces metabolic and mitochondrial alterations that are exacerbated by anomalies in PINK1/Parkin-mediated mitophagy, causing the accumulation of dysfunctional mitochondria that trigger epithelial stress and ultimately cell damage. Using drug-disease network perturbation modelling, we predict targetable pathways, whose modulation repairs mitochondrial dysfunctions in patient-derived cells and alleviate phenotype changes in mmut-deficient zebrafish. These results suggest a link between primary MMUT deficiency, diseased mitochondria, mitophagy dysfunction and epithelial stress, and provide potential therapeutic perspectives for MMA. 1 1234567890():,;Mitochondrial dysfunction drives stress in MMA cells. As MMUT deficiency alters mitochondrial homeostasis, we next assessed potential consequences on mitochondrial function. Consistent with increased numbers of morphologically aberrant mitochondria, the mitochondrial membrane potential (Δψ m ) was drastically reduced in MMA cells (Fig. 2d), as evidenced by live cell imaging analyses of the mitochondrial network with cellpermeant, fluorescent dye tetramethylrhodamine methyl ester (TMRM, which readily accumulates within functional mitochondria) and MitoTracker (a fluorescent probe that localizes to mitochondria). These changes were paralleled by a major mitochondrial oxidative stress ( Fig. 2e), as testified by the elevated production of mitochondria (mt)-derived ROS (MitoSOX, a livecell-permeant indicator of mitochondrial ROS) and augmented antioxidant response (SOD1; Fig. 2g). Treatment with the mitochondrial complex I inhibitor Rotenone (5 μM for 24 h), which ARTICLE NATURE COMMUNICATIONS | https://doi.