Staphylococcus aureus is one of the most frequent human pathogens that can also act as a facultative intracellular pathogen causing infections that are extremely difficult to treat. Only little is known about the pathogen's intracellular adaptation strategies to escape the host's response. Here, we present an advanced Raman-based imaging approach providing high quality false-color images to specifically identify intracellular S. aureus and to localize them exactly in three dimensions within endothelial cells. At the same time unprecedented insights into the metabolic characteristics of the pathogen are provided in a label-free and nondestructive manner. The spectral information reveals that the intracellular bacteria are in the exponential growth phase with a reduced replication rate and biochemically different from extracellular bacteria proving their adaptation to the host's conditions. This powerful biophotonic analysis tool paves the way for further mechanistic studies of difficult-to-investigate infection processes.