Abstract Damage to the underlying Si substrate during the over-etching step of SiN atomic layer etching (ALE) was investigated. CH3F/Ar plasma was applied in the adsorption step, and Ar plasma in the desorption step. ALE increased interface trap density (D _it), whereas Ar plasma did not affect D _it. C, H, and F in the hydrofluorocarbon polymer, knocked-on by Ar, penetrated the Si substrate, which resulted in an increase in D _it. Additionally, H in the polymer layer had a negligible impact on the damage caused by ALE. The H-penetration depth was shallow because the energy transferred from Ar to the H component in the polymer was low. Damage occurred only in the first cycle of ALE because a thick polymer layer, deposited after the second cycle, protected the substrate from additional damage. Thus, precise control of incident ion energy, adsorbed polymer thickness, and polymer composition are required to realize low-damage ALE.