In the spinel compound GeCo$_2$O$_4$, the Co$^{2+}$ pyrochlore sublattice presents remarkable magnetic field-induced behaviors that we unveil through neutron and X-ray single-crystal diffraction. The Neel ordered magnetic phase is entered through a structural lowering of the cubic symmetry. In this phase, when a magnetic field is applied along a 2-fold cubic direction, a spin-flop transition of one fourth of the magnetic moments releases the magnetic frustration and triggers magnetostructural effects. At high field, these ultimately lead to an unusual spin reorientation associated to structural changes.