The analysis of phagolysosomes within professional phagocytic cells is facilitated by their isolation. Here, we optimized a protocol for the isolation of intact phagolysosomes from macrophages infected with the spores of Aspergillus fumigatus. Purified phagolysosomes allow improved immunostaining, e.g., of phagolysosomal membrane proteins, or proteome analysis. For complete details on the use and execution of this protocol, please refer to Schmidt et al. (2020).