We compare the abundances of various chemical species as derived with 3D hydrodynamical and classical 1D stellar atmosphere codes in a late-type giant characterized by Teff =3640 K, log g = 1.0, [M/H]= 0.0. For this particular set of atmospheric parameters the 3D–1D abundance differences are generally small for neutral atoms and molecules but they may reach up to 0.3–0.4 dex in case of ions. The 3D–1D differences generally become increasingly more negative at higher excitation potentials and are typically largest in the optical wavelength range. Their sign can be both positive and negative, and depends on the excitation potential and wavelength of a given spectral line. While our results obtained with this particular late-type giant model suggest that 1D stellar atmosphere models may be safe to use with neutral atoms and molecules, care should be taken if they are exploited with ions.