Differential rotation induced by the r-mode instability can generate very strong toroidal fields in the core of accreting, millisecond spinning neutron stars. We introduce explicitly the magnetic damping term in the evolution equations of the r-modes and solve them numerically in the Newtonian limit, to follow the development and growth of the internal magnetic field. We show that the strength of the latter can reach large values, B ∼ 10 14 G, in the core of the fastest accreting neutron stars. This is strong enough to induce a significant quadrupole moment of the neutron star mass distribution, corresponding to an ellipticity |ǫB| ∼ 10 −8 . If the symmetry axis of the induced magnetic field is not aligned with the spin axis, the neutron star radiates gravitational waves. We suggest that this mechanism may explain the upper limit of the spin frequencies observed in accreting neutron stars in Low Mass X-Ray Binaries. We discuss the relevance of our results for the search of gravitational waves.