We present an electrochemical sandwich-type assay based on the splitting of an aptamer into two fragments. Gold nanoparticles are modified with one of the fragments and a redox polyelectrolyte. The first is used as the recognition element, while the other for the electrochemical signal generation. The split-aptamer used here can detect adenosine, used as a model system for recognizing small molecules. The multiple binding sites on the nanoparticle, along with the high number of redox probes, yield a selective and sensitive assay for adenosine, achieving a limit of detection of 3.1 nM and a linear range up to 75 nM. The obtained results are analyzed in terms of the nanoparticle and electrode architectures. The assay can be easily extended to other small molecules and sandwich assays, representing a promising tool for detecting metabolites at the nanomolar level.