Macrophages tightly scale their core metabolism upon activation, but the precise regulation of the mitochondrial electron transport chain (ETC) and its functional implications are currently unknown. Here we show that recognition of live bacteria by macrophages transiently decreased the assembly of ETC complex I (CI) and CI-containing supercomplexes and switched the relative contribution of CI and CII to mitochondrial respiration. This was mediated by the phagosomal NADPH-oxidase and the reactive oxygen species (ROS)-dependent tyrosine-kinase Fgr. It required Toll-like receptor signalling and the NLRP3 inflammasome, which were both connected to bacterial viability-specific immune responses. Inhibition of CII during E. coli infection normalized serum levels of interleukin 1β (IL-1β) and IL-10 to levels found in mice treated with dead bacteria, and impaired control of bacteria. We thus identified ETC adaptations as an early immune-metabolic checkpoint that adjusts innate immune responses to bacterial infection.