Abstract <p>This work presents data on the X-ray diffraction analysis of air-dry, water-saturated, and working samples of the MFFK-G-025 and MMK-045 membranes obtained during microfiltration separation of process solutions. A decrease in crystallinity of the membrane samples is noted during their water saturation and operation, which affects the microfiltration separation of process solutions. The reduced peak intensities of the bands are analyzed in the X-ray diffraction patterns. Five distinct reflections responsible for the crystallinity of the membrane and four amorphous halos are observed in the diffraction patterns of all MFFK-G-025 membrane samples, and two distinct reflections responsible for the crystallinity of the membrane and two amorphous halos are visible in the MMK-045 membrane samples. The crystallinity of the MFFK-G-025 membrane decreased from 58.16 to 36.83, and that of the MMK-045 membrane from 33.51 to 20.21. The decrease in peak intensity in the diffraction patterns of working membrane samples compared to air-dry ones indicates a change in the structure of water in the membrane itself: molecular water becomes weakly bound liquid water. It can be assumed that the structural rearrangement of the macromolecules of the active layer of the MFFK-G-025 and MMK-045 membranes affects their conformation, i.e., a redistribution of the ratio of amorphous and crystalline segments of the membranes occurs.</p>