Surface of magnetic silica nanoparticles is modified by grafting with carboxymethyl-β-cyclodextrin (CM-β-CD) via carbodiimide activation. The functionalized magnetic core-shell nanoparticles (MNPs) are characterized by Transmission Electron Microscopy (TEM), Fourier Transform Infra Red (FTIR) spectroscopy, X-ray Diffraction (XRD), X-ray Photoelectron Spectroscopy (XPS) and Vibrating Sample Magnetometer (VSM). These nano-sized particles are scrutinized for adsorption of certain chiral aromatic amino acid enantiomers namely, d- and l-tryptophan (Trp), d- and l-phenylalanine (Phe) and d- and l-tyrosine (Tyr) from phosphate buffer solutions. Adsorption capacities of the coated magnetic nanoparticles toward amino acid enantiomers are in the order: l-Trp>l-Phe>l-Tyr and under the same condition, adsorption capacities are higher for l-enantiomers than the corresponding d-enantiomers. All the equilibrium adsorption isotherms are fitted well to Freundlich model. FTIR studies depict significant changes after adsorption of amino acids onto nanoparticles. The stretching vibration frequencies of NH bonds of the amino acid molecules are changed with complex formation through host-guest interaction. The structure and hydrophobicity of amino acid molecules emphasize the interactions between amino acid molecules and the nano-adsorbents bearing cyclodextrin, thus play important roles in the difference of their adsorption behaviors.