Structural defects on an atomic level can crucially impact the magnetic properties of a material. We study this phenomenon by means of magnetometry and powder neutron diffraction on a stoichiometric, monoclinic pyrrhotite (Fe7S8), which is a classic omission structure with a magnetic anomaly at about 30 K. The initial structural distortion of the pyrrhotite at 300 K caused by the vacancy arrangement decreases upon cooling, and simultaneous to the magnetic anomaly the anisotropic contraction of the unit cell homogenizes the covalency of the Fe-Fe bonds with lengths less than 3.0 Å and the Fe-S-Fe bond angles. These changes on the atomic level affect the spin-orbit coupling and the super-exchange interactions in Fe7S8, and trigger the low-temperature magnetic anomaly within a crystallographically stable system.