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Summary: In hypoxic and inflamed tissues, oxygen (O2)-dependent antimicrobial defenses are impaired due to a shortage of O2. To gain insight into the mechanisms that control bacterial infection under hypoxic conditions, we infected macrophages with the obligate intracellular pathogen Coxiella burnetii, the causative agent of Q fever. Our experiments revealed that hypoxia impeded C. burnetii replication in a hypoxia-inducible factor (HIF) 1α-dependent manner. Mechanistically, under hypoxia, HIF1α impaired the activity of STAT3, which in turn reduced the intracellular level of TCA cycle intermediates, including citrate, and impeded C. burnetii replication in macrophages. However, bacterial viability was maintained, allowing the persistence of C. burnetii, which is a prerequisite for the development of chronic Q fever. This knowledge will open future research avenues on the pathogenesis of chronic Q fever. In addition, the regulation of TCA cycle metabolites by HIF1α represents a previously unappreciated mechanism of host defense against intracellular pathogens. : The mechanisms that control bacterial infection under hypoxic conditions are only partially understood. Hayek et al. show that hypoxia-mediated stabilization of HIF1α results in the inhibition of STAT3 activation and the reduction of TCA metabolite levels, including citrate, in macrophages. This prevents C. burnetii replication without reducing bacterial viability. Keywords: Coxiella burnetii, HIF1α, STAT3, citrate, macrophage