Herein, we report on the study of supramolecular assemblies based on polyoxometalates (POMs) upon their modification with amino acids. Two POM-amino acid hybrids were synthesized by coupling a functionalized Keggin type polyoxoanion [PW11O39{Sn(C6H4)C[triple bond, length as m-dash]C(C6H4)COOH}]4- with carboxyl-protected (methyl-ester) phenylalanine or diphenylalanine peptides. Surprisingly, all compounds, including the initial POM, formed supramolecular nanospheres in different solvent mixtures, which were examined by scanning electron microscopy (SEM). Molecular dynamics (MD) simulations for the POM-amino acid species revealed that the hydrophobic forces are mainly responsible for the initial aggregation into incipient micelle type structures, in which the organic arms are buried inside the aggregate while POM polar heads are more exposed to the solvent with tetrabutyl-ammonium counter cations acting as linkers.