Coxiella burnetii, the etiological agent of the zoonotic infection Q fever, is an obligate intracellular bacterial pathogen that replicates inside the lysosome-derived Coxiella-containing vacuole (CCV). The CCV maintains the hydrolytic and acidic nature of the host lysosome despite C. burnetii directing the massive expansion of this compartment to accommodate the replicating pathogen. To establish this unique replicative niche, C. burnetii utilizes the Dot/Icm type IV secretion system to translocate approximately 150 effectors into the host cell that modulate various cellular processes. In order to characterize the host-pathogen interactions that occur during C. burnetii infection, SILAC based proteomics was performed to examine changes in the host proteome during infection of THP-1 cells. This proteomic analysis showed that during C. burnetii infection, the abundance of many proteins involved in host cell autophagy and lysosome biogenesis was increased. Given this finding, the role of host transcription factor’s TFEB and TFE3, that regulate the expression of a network of genes involved in autophagy and lysosomal biogenesis, was examined. Three days post-infection with C. burnetii both TFEB and TFE3 were activated as demonstrated by their trafficking from the cytoplasm into the nucleus. Nuclear to cytoplasmic ratio of TFEB and TFE3 was measured using a custom ImageJ macro. The nuclear translocation of these transcription factors appears to be controlled by C. burnetii as blocking bacterial translation with chloramphenicol led to TFEB and TFE3 movement back into the cytoplasm. siRNA silencing of tfeb and tfe3 demonstrated that these transcription factors are important for CCV expansion suggesting they play a role in the intracellular success of C. burnetii.