Primary mitochondrial diseases (PMDs) associate with pediatric neurological disorders and are traditionally related to oxidative phosphorylation system (OXPHOS) defects in neurons. Interestingly, both PMD mouse models and patients also show gliosis, and pharmacologic depletion of microglia, the brain resident innate immunity, ameliorate the multiple symptoms of a mouse model. Since microglia activation correlates with the expression of OXPHOS genes, we studied whether OXPHOS deficits in microglia may contribute to PMDs. We first observed that the metabolic rewiring associated to microglia IL-33 stimulation in vitro, was partially changed by complex I (CI) inhibition (rotenone treatment)a. In vivo, we generated a mouse model deficient for CI activity in microglia (MGcCI)b. MGcCI microglia showed metabolic rewiring and gradual transcriptional activationc, which leads to hypertrophy and dysfunction in juvenile (1-month-old) and adult (3-month-old) stagesd, respectively. These dysfunctional microglia were characterised by a significant reduction of phagocytic ability and microglial death, both two determined by CAS3 immunostaininge. MGcCI mice presented widespread reactive astrocytesf, a decrease of synaptic markers VGLUT and VGATg accompanied by increased number of parvalbumin neurons and Pvalb reduced expressionh. They showed behavioral deficit characterized by prolonged periods of immobility, loss of weight, and premature death that was partially rescued by pharmacologic depletion of microgliai. Our data demonstrate that microglia development depends on OXPHOS and suggest a direct microglial contribution to PMDs.