Grain boundary segregation is a critical issue in materials science because it determines the properties of individual grain boundaries and thus governs the macroscopic properties of materials. Recent progress in electron microscopy has greatly improved our understanding of grain boundary segregation phenomena down to atomistic dimensions, but solute segregation is still extremely challenging to experimentally identify at the atomic scale. Here, we report direct observations of atomic-scale yttrium solute segregation behaviours in an yttria-stabilized-zirconia grain boundary using atomic-resolution energy-dispersive X-ray spectroscopy analysis. We found that yttrium solute atoms preferentially segregate to specific atomic sites at the core of the grain boundary, forming a unique chemically-ordered structure across the grain boundary.