Neutron diffraction measurements on multiferroic LuFe₂O₄ show changes in the antiferromagnetic (AFM) structure characterized by wave vector q=(1/3 1/3 1/2) as a function of electric field cooling procedures. The increase of intensity from all magnetic domains and the decrease in the two-dimensional (2D) magnetic order observed below the Néel temperature are indicative of increased ferroelectric charge order (CO). The AFM order changes the dynamics of the CO state, and stabilizes it. It is determined that the increase in electric polarization observed at the magnetic ordering temperature is due to a transition from paramagnetic 2D charge order to AFM three-dimensional charge order.