Coxiella burnetii is a Gram-negative bacterium which causes Q fever, a complex and life‑threatening infection with both acute and chronic presentations. C. burnetii replicates within a unique vacuole derived from the host cell lysosome and little is known about the utilisation of carbon sources by C. burnetii within this compartment. Here we used 13C‑stable isotope labelling to investigate central carbon metabolism of axenically and intracellularly cultivated C. burnetii bacterium, at both log and stationary phases of growth. Important differences in utilisation of the 13C-glucose and 13C‑glutamate substrates across the two growth conditions, and at the two different growth stages, were observed. Both bacterial populations were capable of using 13C-glucose and 13C‑glutamate as carbon sources, with observed labelling of intermediates in glycolysis and gluconeogenesis, respectively, and in the TCA cycle. This demonstrates that C. burnetii maintains metabolic flexibility even within the unique intracellular replicative niche. Characterisation of the putative C. burnetii glucose transporter, CBU0265, led to a significant decrease in 13C‑glucose utilisation, but did not abolish glucose usage, suggesting that C. burnetii express additional hexose transporters. Intracellular infection of human cells and in vivo studies in the insect model showed that loss of CBU0265 had no impact on intracellular replication or virulence. These analyses demonstrate that C. burnetii are able to use multiple carbon sources in vivo and contribute important understanding of how this unique pathogen replicates within the harsh lysosome‑derived vacuole.