A significant amount of scandium (Sc) has been found in the laterites developed over ultramafic and mafic rocks, but much less knowledge is available regarding Sc speciation in laterites. The geochemistry of Sc is unique compared with other rare earth elements (REE), however, the controls of their different partitioning behaviors are still poorly understood. In this study, the distribution and speciation of Sc and yttrium (Y) in the Philippine nickel (Ni) laterites were determined by a combination of sequential extraction, synchrotron-based micro-focused X-ray fluorescence (mu-XRF) and X-ray absorption fine structure (XAFS) techniques, to clarify different geochemical behaviors between Sc and other REE in Ni laterites. Here we demonstrate that Sc can be structurally incorporated into goethite in Ni laterites apart from the adsorption on the goethite surface, while Y is mainly adsorbed on goethite via the bidentate-binuclear inner-sphere complexation. The striking disparity regarding the speciation could result from ionic radius of Sc3+ and Y3+ (REE3+) with respect to Fe3+ in iron (oxyhydr)oxides, which is likely responsible for the relatively lower mobilization and (re)distribution of Sc than other REE in Ni laterites. Our study firstly reports disparate chemical speciation of Sc and Y in Ni laterites and provides molecular-scale insights into the control of different solubility and partitioning behaviors of Sc and other REE.