This research describes the development of a multi-analyte lateral-flow immunoassay intended for the simultaneous detection of three anti-protozoan drugs (coccidiostats). These drugs, namely, halofuginone, toltrazuril and diclazuril, are used in the treatment of Eimeria spp. infections in cattle, pigs, chickens and turkeys. Coloured carboxylated microspheres were coated with each of the detection antibodies and employed in a lateral-flow assay format for detection of these residues in eggs. Using this approach, halofuginone was detectable at a limit of 10 ng/mL or greater, toltrazuril at 100 ng/mL and, similarly, diclazuril had a detection limit of 100 ng/mL, which is below the maximum allowed residue limit for all three as outlined by EU regulation. This simple cost-efficient assay and analysis method could pave the way for more efficient simultaneous monitoring of small-molecule residues in the future.