The surface-atom Casimir-Polder-Lifshitz force out of thermal equilibrium is investigated in the framework of macroscopic electrodynamics. Particular attention is devoted to its large distance limit that shows a new, stronger behaviour with respect to the equilibrium case. The frequency shift produced by the surface-atom force on the the center-of-mass oscillations of a harmonically trapped Bose-Einstein condensate and on the Bloch oscillations of an ultra-cold fermionic gas in an optical lattice are discussed for configurations out of thermal equilibrium.