Dictyostelium discoideum is a professional phagocyte using phagocytosis to feed on bacteria. It is used as a surrogate macrophage to study phagocytosis mechanisms and as a host model organism to study intracellular bacterial infections. Mycobacterium marinum, as its close cousin M. tuberculosis, infects innate immune cells where it stops the maturation of its residing-phagosome to prevent its killing and to establish a compartment where it can replicate. In the following work, we have used the host-pathogen model system D. discoideum-M. marinum to better understand how M. marinum manipulates the maturation of its containing-phagosome. We have established a procedure to isolate mycobacteria-containing compartments. Then, using isobaric labelling and mass spectrometry, we studied quantitative proteomic modifications applied to the M. marinum-containing compartment during the first hours of infection. We also compared the quantitative proteomic composition of compartments containing the pathogenic strain M. marinum to compartments containing non-pathogenic, avirulent or attenuated mycobacteria strains.