The Bi 3 FeMo 2 O 12 system is examined as a rare example of a transition-metal oxide which, upon heating, undergoes a symmetry lowering and a 2:1 ordering of the transition-metal cations. The compound was synthesized in the tetragonal scheelite structure (S.G. #88: I4 1 /a) by a sol−gel method and converted into the monoclinic polymorph (S.G. #15: C2/c) by calcination above 500 °C. The structure of both polymorphs was analyzed using a combination of X-ray and neutron diffraction data, and the temperature-dependent phase transition between these was investigated in situ using variable-temperature neutron powder diffraction and scanning transmission electron microscopy. The results show that the structural phase transition takes place at low temperatures (∼500 °C) and is first order in nature, as evident from the coexistence of both structures. The transition from tetragonal to monoclinic results in the reduction of the equivalent unit cell volume. The role of the Bi 3+ 6s lone pairs in the temperature-driven phase transition has been studied using neutron pair distribution function analysis. Local structure analysis via neutron total scattering revealed the Bi 3+ 6s lone pairs to be stereochemically active in both structures, with short correlation lengths in the tetragonal structure and long correlation lengths in the monoclinic structure, leading to facile phase conversion and to a more efficient packing density with highly correlated lone pairs in the monoclinic structure. Magnetization isotherms of the tetragonal structure collected at 1.8 K exhibit ferromagnetic behavior, suggesting that the interplay between the observed short-range monoclinic order, defects, and surface-to-bulk effects alters the magnetic interaction, leading to short-range ferromagnetic interactions, which is highly unexpected given the low-temperature antiferromagnetic order observed in the monoclinic structure.