Possible mechanisms of etch-stops in plasma-enhanced atomic layer etching (PE-ALE) for silicon nitride (SiN) were examined with molecular dynamics (MD) simulations. Recent experiments [Hirata et al., J. Vac. Sci. Technol. A 38, 062601 (2020)] have shown that the PE-ALE process of SiN consisting of hydro-fluorocarbon (HFC) adsorption and argon ion (Ar+) irradiation can lead to an etch-stop. The MD simulations have revealed that carbon (C) remnants at the end of a PE-ALE cycle can enhance further accumulation of C in the subsequent cycle. Under typical Ar+ ion irradiation conditions, nitrogen (N) atoms are preferentially removed from the surface over silicon (Si) atoms, and therefore, the SiN surface becomes more Si rich, which also promotes C accumulation by the formation of Si–C bonds. It is also seen that fluorine atoms contribute to the removal of Si, whereas hydrogen and C atoms contribute to the removal of N from the SiN surface.