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Abstract We compute the transverse and longitudinal diffractive structure functions to full next-to-leading order accuracy in the dipole picture of deep inelastic scattering. Our calculation uses the standard light-cone perturbation theory method for the partonic content of the virtual photon, together with the Color Glass Condensate description of the target color field. Our result includes as a subset the $$q\overline{q }g$$ contribution calculated earlier. We show that there is a rapidity divergence that can be factorized into the BK/JIMWLK evolution of the target Wilson lines, and that all other divergences cancel.