The modification of steel (AISI 316L and AISI 4140) surface morphology and underlying inter-crystalline grains strain due to Xe$^+$ ion bombardment are reported to affect nitrogen diffusion after a pulsed plasma nitriding process. The ion bombardment induces regular nanometric patterns and increases the roughness of the material surface. The strain induced by the noble gas bombardment is observed in depths which are orders of magnitude larger than the projectiles stopping distance. The pre-bombarded samples show peculiar microstructures formed in the nitrided layers, modifying the in-depth hardness profile. Unlike the double nitrided layer normally obtained in austenitic stainless steel by pulsed plasma nitriding process, the Xe$^+$ pre-bombardment treatment leads to a single thick compact layer. In nitrided pre-bombarded AISI 4140 steel, the diffusion zone shows long iron nitride needle-shaped precipitates, while in non-pre-bombarded samples finer precipitates are distributed in the material.