GRB 100418A was an intermediate duration GRB detected by Swift. It showed an initially dim optical afterglow that had a late increase in brightness, reaching its maximum several hours after the burst onset, unlike typical afterglows that peak tens of seconds after. It also displayed a bright X-ray and radio counterpart. In this paper we present the observations of the afterglow obtained with X-shooter. Three epochs were obtained, 0.4, 1.4, and 2.4 days after the burst. In these spectra, each covering the range from 3000 to 24800 Å, we detect abundant absorption features with 4 velocity components, and emission lines from the host galaxy with 2 additional velocity components. In one single velocity component, we detect a Fe II* 2396 Å fine structure feature which disappears from the first to the second epoch indicating that it is due to the effect of the GRB radiation on its environment. We consider it to be the closest absorption component to the GRB itself, for which we determine a redshift of z=0.6239±0.0002. From the Hα to [N II] ratio we determine a host galaxy metallicity of 0.5 solar.