We investigate the effect of a pinned superfluid component on the gravitational wave emissions of a rotating neutron star. The pinning of superfluid vortices to the flux-tubes in the outer core (where the protons are likely to form a type-II superconductor) is a possible mechanism to sustain long-lived and non-axisymmetric neutron currents in the interior, which break the axial symmetry of the unperturbed hydrostatic configuration. We consider pinning-induced perturbations to a stationary corotating configuration and determine the upper limits on the strength of gravitational wave emissions due to the pinning of vortices with a strong toroidal magnetic field of the kind predicted by recent magneto-hydrodynamic simulations of neutron star interiors. We estimate the contributions to gravitational wave emissions from both the mass and current multipole generated by the pinned vorticity in the outer core and find that the mass quadrupole can be large enough for gravitational waves to provide the dominant spindown torque in millisecond pulsars.