We investigate the emergence of anti-ferromagnetic ordering and its effect on the helical edge states in a quantum spin Hall insulator, in the presence of strong Coulomb interaction. Using dynamical mean-field theory, we show that the breakdown of lattice translational symmetry favours the formation of magnetic ordering with non-trivial spatial modulation. The onset of a non-uniform magnetization enables the coexistence of spin-ordered and topologically non-trivial states. An unambiguous signature of the persistence of the topological bulk property is the survival of bona fide edge states. We show that the penetration of the magnetic order is accompanied by the progressive reconstruction of gapless states in sub-peripherals layers, redefining the actual topological boundary within the system.