We present an abundance analysis of the low-metallicity benchmark red giant star HD 122563 based on realistic , state-of-the-art , high-resolution , three-dimensional ( 3D ) model stellar atmospheres including non-grey radiative transfer through opacity binning with four , twelve , and 48 bins . The 48-bin 3D simulation reaches temperatures lower by \sim 300 - 500 K than the corresponding 1D model in the upper atmosphere . Small variations in the opacity binning , adopted line opacities , or chemical mixture can cool the photospheric layers by a further { \sim } 100 - 300 K and alter the effective temperature by { \sim } 100 K . A 3D local thermodynamic equilibrium ( LTE ) spectroscopic analysis of \ion Fei and \ion Feii lines gives discrepant results in terms of derived Fe abundance , which we ascribe to non-LTE effects and systematic errors on the stellar parameters . We also determine C , N , and O abundances by simultaneously fitting CH , OH , NH , and CN molecular bands and lines in the ultraviolet , visible , and infrared . We find a small positive 3D - 1D abundance correction for carbon ( +0.03 dex ) and negative ones for nitrogen ( -0.07 dex ) and oxygen ( -0.34 dex ) . From the analysis of the [ \ion Oi ] line at 6300.3 Å , we derive a significantly higher oxygen abundance than from molecular lines ( +0.46 dex in 3D and +0.15 dex in 1D ) . We rule out important OH photodissociation effects as possible explanation for the discrepancy and note that lowering the surface gravity would reduce the oxygen abundance difference between molecular and atomic indicators .