In this research magnetic hybrid nanomaterials modified with morin for sorption of scandium ions have been synthesized and investigated. In general, sorption of scandium increases with increasing pH. However, Fe@COO-morin nanocomposite with covalently bonded morin showed superiority over physically coated Fe3O4@morin nanoparticles. Several models have been applied for investigation of different aspects of sorption onto Fe@COO-morin. Results show, that it follows Langmuir model and pseudo-second order kinetics. Developed hybrid Fe@COO-morin nanoparticles were successfully applied for separation and preconcentration of scandium using magnetic solid phase extraction from spiked water samples. Optimized procedure includes selective sorption of scandium at pH 5, elution with 1 mol L−1 HNO3 and ICP OES determination. A preconcentration factor of 20 was achieved and sorbent provides the possibility of multiple use.