Ttrioctylphosphine oxide (TOPO) stabilized CdSe/ZnS quantum dots (QD) were modified with 6-ferrocenyl-1-hexanethiol (FcHT) or 11-ferrocenyl-1-undecanethiol (FcUT) via ligand exchange. The presence of ferrocenyl thiol ligands on the surface of the QDs was proven by diffusion ordered NMR spectroscopy. Upon replacement of the initial TOPO ligand with ferrocene derivatives the emission of the QDs decreased. Phase transfer of ferrocene-modified QDs from organic solvents into water was achieved by complexation reactions with β-cyclodextrin (β-CD). The QDs coated with ferrocene thiols are soluble in nonpolar solvents and are transferred into the aqueous phase upon formation of host−guest complexes between the ferrocene units and the cavity of β-CD. The reversibility of the phase transfer was probed by the addition of naphthalene and adamantane derivatives to the aqueous phase containing QD-[Fc-CD] adduct.