ABSTRACT The spin distribution of accreting neutron stars in low-mass X-ray binary systems shows a concentration of pulsars well below the Keplerian break-up limit. It has been suggested that their spin frequencies may be limited by the emission of gravitational waves, due to the presence of large-scale asymmetries in the internal temperature profile of the star. These temperature asymmetries have been demonstrated to lead to a non-axisymmetric mass distribution, or ‘mountain’, that generates gravitational waves at twice the spin frequency. The presence of a toroidal magnetic field in the interior of accreting neutron stars has been shown to introduce such anisotropies in the star’s thermal conductivity, by restricting the flow of heat orthogonal to the magnetic field and establishing a non-axisymmetric temperature distribution within the star. We revisit this mechanism, extending the computational domain from (only) the crust to the entire star, incorporating more realistic microphysics, and exploring different choices of outer boundary condition. By allowing a magnetic field to permeate the core of the neutron star, we find that the likely level of temperature asymmetry in the inner crust (ρ ∼ 1013 g cm−3) can be up to 3 orders of magnitude greater than the previous estimate, improving prospects for one day detecting continuous gravitational radiation. We also show that temperature asymmetries sufficiently large to be interesting for gravitational wave emission can be generated in strongly accreting neutron stars if crustal magnetic fields can reach ∼1012 G.