Peptidomimetic and anti-immunocomplex peptides, which can be readily isolated from a phage-display library, have shown great potential for small-molecule immunoassay development because they typically improve the sensitivity and avoid the use of chemical haptens as coatings or tracer antigens. However, phage-borne peptides are unconventional immunoassay reagents, which greatly limits their use in commercial applications, and require secondary reagents for detection. In order to overcome these limitations, we used C2-15, a peptidomimetic of imidaclothiz, as a model peptide fused to emerald-green fluorescent protein (EmGFP) at the N-terminus (C2-15-EmGFP) and C-terminus (EmGFP-C2-15) to generate novel fluorescent-peptide tracers. Both recombinant fluorophores reacted with similar affinity to the anti-imidaclothiz monoclonal antibody 1E7, but because of its higher expression, C2-15-EmGFP was chosen to develop a competitive magnetic-separation fluorescence immunoassay (MSFIA). After a competitive step with the analyte, the C2-15-EmGFP-antibody complex bound to the magnetic beads was separated with a magnet, and because of the fast dissociation of the peptide-antibody interaction, the fluorescence signal was detected following the spontaneous dissociation of the complex in fresh buffer. The concentration of imidaclothiz causing the 50% inhibitory concentration (IC50) was 11.00 ng mL-1, and the MSFIA performed with excellent recovery and had a good correlation with high-performance liquid chromatography in different matrices.