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Abstract We report an unconventional effect of synchrotron X-ray irradiation in which Co–O bonds in thermally annealed (Y, Co)-codoped CeO2 nanocrystal samples were formed due to, instead of broken by, X-ray irradiation. Our experimental data indicate that escaping oxygen atoms from X-ray-broken Ce–O bonds may be captured by Co dopant atoms to form additional Co–O bonds. Consequently, the Co dopant atoms were pumped by X-rays from the energetically-favored thermally-stable Co-O4 square-planar structure to the metastable octahedral Co-O6 environment, practically a reversal of thermal annealing effects in (Y, Co)-codoped CeO2 nanocrystals. The band gap of doped CeO2 with Co dopant in the Co-O6 structure was previously found to be 1.61 eV higher than that with Co in the Co-O4 environment. Therefore, X-ray irradiation can work with thermal annealing in opposing directions to fine tune and optimize the band gap of the material for specific technological applications.