Effects of the Verwey transition on the (100) surface of magnetite were studied using scanning tunelling microscopy and spin polarized low-energy electron microsccopy. On cooling through the transition temperature Tv, the initially flat surface undergoes a roof-like distortion with a periodicity of ~0.5 um due to ferroelastic twinning within monoclinic domains of the low-temperature monoclinic structure. The monoclinic c axis orients in the surface plane, along the c directions. At the atomic scale, the charge-ordered sqrt2xsqrt2R45 reconstruction of the (100) surface is unperturbed by the bulk transition, and is continuous over the twin boundaries. Time resolved low-energy electron microscopy movies reveal the structural transition to be first-order at the surface, indicating that the bulk transition is not an extension of the Verwey-like sqrt2xsqrt2R45 reconstruction. Although conceptually similar, the charge-ordered phases of the (100) surface and sub-Tv bulk of magnetite are unrelated phenomena.