This paper reports the synthesis of a trifluoroethylester-PEG-thiol ligand (TFEE-PEG-SH) and its use to create water-soluble, chemically functional Au metal and FePt magnetic nanoparticles. The trifluoroethylester terminus facilitates attachment of any primary-amine-containing molecule via amide bond formation at room temperature without the use of coupling agents. Three possible routes of nanoparticle functionalization are demonstrated: synthesis of Au nanoparticles in the presence of functionalized R-PEG-SH; ligand-exchange of R-PEG-SH onto both Au and FePt nanoparticles; and exchange of TFEE-PEG-SH onto Au nanoparticles followed by subsequent amide condensation. A series of primary-amine-containing molecules, including biotin and fluorescamine, are easily attached to the water-soluble particles, and the resulting materials are characterized by NMR, UV-visible absorption, and emission spectroscopies.