In order to highlight the applications of bioflavonoids in materials chemistry, naringin and its chalcone form were used in the nanomaterial synthesis to produce flavonoid-conjugated nanomaterials in aqueous phase. Chalcone form proved to be excellent reducing as well as stabilizing agent in the synthesis of monodisperse Au, Ag, and Pd nanoparticles (NPs) of ∼5-15 nm, following in situ reaction conditions where no external reducing or stabilizing agents were used. The mechanism of NP surface adsorption of flavonoid was determined with the help of dynamic light scattering and zeta potential measurements. Surface-adsorbed flavonoids also allowed NPs to easily transfer into the organic phase by using aqueous insoluble ionic liquid. Pd NPs attracted the excessive amount of surface adsorption of both naringin as well as its chalcone form that in turn drove Pd NPs in self-assembled state in comparison to Au or Ag NPs. An amount of surface-adsorbed flavonoids selectively determined the extraction of protein fractions from complex zein corn starch protein solution. Self-assembled Pd NPs with a large amount of surface-adsorbed naringin preferentially extracted zein fraction of higher molar mass, whereas Au and Ag NPs almost equally extracted the zein fractions of lower molar masses.