This study demonstrates a relationship between changes of magnetic susceptibility and microstructure developing in minerals of a magnetite‐bearing ore, experimentally shocked to pressures of 5, 10, 20, and 30 GPa. Shock‐induced effects on magnetic properties were quantified by bulk magnetic susceptibility measurements while shock‐induced microstructures were studied by high‐resolution scanning electron microscopy. Microstructural changes were compared between magnetite, quartz, amphibole, and biotite grains. In the 5 GPa sample, a sharp drop of magnetic susceptibility correlates with distinct fragmentation as well as with formation of shear bands and twins in magnetite. At 10 GPa, shear bands and twins in magnetite are accompanied by droplet‐shaped nanograins. In this shock pressure regime, quartz and amphibole still show intensive grain fragmentation. Twins in quartz and foam‐shaped, highly porous amphibole are formed at 20 and 30 GPa. The formation of porous minerals suggests that shock heating of these mineral grains resulted in localized temperature spikes. The identified shock‐induced features in magnetite strongly advise that variations in the bulk magnetic susceptibility result from cooperative grain fragmentation, plastic deformation and/or localized amorphization, and probably postshock annealing. In particular, the increasing shock heating at high pressures is assumed to be responsible for a partial defect annealing which we suggest to be responsible for the almost constant values of magnetic susceptibility above 10 GPa.