We describe a pyrophosphate (PPi) probe that is based on a fluorescent dicarboxylate-substituted poly(para-phenyleneethynylene) (PPE) and 10 nm cobalt–iron spinel nanoparticles (NPs) in aqueous media. The spinel NPs efficiently quench the fluorescence of the PPE at a concentration of 20–30 pmol. Addition of phosphate anions to the PPE–NP construct displaces the quenched PPE to give rise to a fluorescent response; we found that PPi and phosphate (Pi) have significantly different binding affinities for the self-assembled materials. We can discern >40 nM PPi in the presence of 0.1 mM Pi at pH 7, which suggests that these assemblies may be useful in bio-analytical applications. This displacement assay was used to effectively determine the ability of pyrophosphatase to hydrolyze PPi to Pi.