Multiplexed measurements of several analytes in parallel using analyte-sensitive organic fluorophores can be hampered by spectral overlap of the different fluorophores. The authors discuss how nanoparticles can help to overcome this problem. First, different organic fluorophores can be separated spatially by confining them to separate containers, each bearing a nanoparticle-based barcode. Second, by coupling different fluorophores to nanoparticles with different fluorescence lifetimes that serve as donors for excitation transfer, the effective fluorescence lifetime of the organic fluorophores as acceptors can be tuned by fluorescence resonance energy transfer (FRET). Thus, the fluorophores can be distinguished by their effective lifetimes. This is an example of how the modification of classical functional materials has already yielded improved and even new functionalities by the integration of nanoparticles with hybrid materials. We outline future opportunities in this area.