Two rationally designed strategies for covalent bonding of fluorescent dyes in coordination polymer nanoparticles aiming to achieve bifunctional fluorescent nanostructures have been developed. The first strategy was based on the synthesis of the coordination polymers structured as nanoparticles by coordination of Co ions to two different catechol ligands containing free functional chemical groups (dopamine and 3,4-dihydroxybenzaldehyde), and a bis(imidazole)-based ligand (1,4-bis(imidazole-1-ylmethyl)benzene, bix). Subsequently, different dyes, namely fluorescein isothiocyanate (FITC), 1-pyrenebutanoic acid hydrazide (PBH) or Alexa Fluor® 568 (A568), could be sequentially attached to the surface of the nanoparticles. The second strategy was focused on the prefunctionalization of catechol ligands with the corresponding dyes and, afterwards, the coordination with the metal ions in presence of bix. In vitro studies demonstrated the internalization of the bifunctional nanoparticles and the persistence of the fluorescent properties after cell uptake without dye leaching.