Mitochondria participate in various cellular processes including energy metabolism, apoptosis, stress responses, inflammation and immunity. While mitochondrial dysfunction contributes to many diseases, mitochondrial perturbations can also be beneficial, a phenomenon coined mitohormesis. We investigated how mitochondrial variation contributes to the heterogeneity of infection outcomes and whether moderate mitochondrial dysfunction could benefit immune-challenged individuals. We took three approaches to model variation in mitochondrial oxidative phosphorylation (OXPHOS) in Drosophila melanogaster: i) inherited natural mitochondrial DNA (mtDNA) variation present in all tissues; ii) sporadic, tissue-specific silencing of OXPHOS-related genes and iii) systemic pharmacological inhibition of OXPHOS, and studied their effects on the cell-mediated innate immune response. When perturbing mitochondrial function, we detected signs of activated cellular innate immunity without infection and upon infection the perturbation caused enhanced immune response. Our data indicate that mitochondrial dysfunction can be beneficial in immune-challenged individuals when it is mild enough and does not cause complications to the host, and ultimately causes variation in infection outcomes between individuals.Author summaryMitochondria are eukaryotic cell organelles involved in various cellular processes including metabolism and cell signaling. The role of mitochondria and the variation of mitochondrial function in immune responses have been increasingly studied across various models. Mitochondrial dysfunction, originating from either the nuclear or the mitochondrial genome, is generally considered harmful for the organism. What is not yet well understood is how immune responses are affected by mitochondrial dysfunction, for example in the context of mitochondrial disease. Here, we show that in the fruit fly Drosophila melanogaster mild systemic or immune cell -specific mitochondrial perturbations enhance the innate immune response of the host to parasitoids. Furthermore, we show that due to the mitochondrial perturbations the cell-mediated immune system of the host is activated in the absence of infection and makes the immune responses more efficient upon infection. Importantly, our results demonstrate that mitochondrial genome variation is one of the underlying factors contributing to the variation in infection outcomes among individuals. Our results therefore contribute to the understanding of innate immunity, by providing information about the genetic causes underlying the variation seen in the response to infections.