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We report on the impact of the nitrogen ion density on the structural and optical properties of GaInNAs quantum wells (QWs) grown by molecular beam epitaxy. The optical emission is strongly increased when the nitrogen ion density is reduced, as we found from photoluminescence experiments. Cathodoluminescence mappings of QWs grown under different ion densities are compared, showing a stronger modulation depth, and thus a higher structural disorder when a higher ion density was present during the growth. Atomic force microscopy measurements of equivalent epilayers showed that ions cause an important structural disorder of the layers. A nearly double root-mean-square roughness is observed when the density of ions is not reduced by external magnetic fields. Additionally, results of transmission electron microscopy measurements of buried GaInNAs QWs are presented, showing that lateral compositional fluctuations of In and N are suppressed when the QWs are protected from the ions. Finally, we find that QWs exposed to higher ion densities during the growth show deeper carrier localization levels and higher delocalization temperatures. These results provide clear evidence that the density of nitrogen ions present in the chamber during the epitaxial growth of GaInNAs QWs directly limits both the structural and optical properties.