Flow cytometry-based immunoassays are valuable in biomedical research and clinical applications due to their high throughput and multianalyte capability, but their adoption in areas such as food safety and environmental monitoring is limited by long assay times and complex workflows. Rapid, simplified bead-based cytometric immunoassays are needed to make these methods viable for point-of-need applications, especially with the increasing accessibility of miniaturized cytometers. This work introduces superparamagnetic hybrid polystyrene-silica core−shell microparticles as promising alternatives to conventional polymer beads in competitive cytometric immunoassays. These beads, featuring high specificity, sensitivity, and excellent handling capabilities via magnetic separation, were evaluated with three different antibodies and binding methods, showing variations in signal intensity based on the antibody and its attachment method. The optimal performance was achieved through a secondary antibody binding approach, providing strong and consistent signals with minimal uncertainty. The optimized protocol made it possible to achieve a detection limit of 0.025 nM in a total assay time of only 15 min and was successfully used to detect ochratoxin A (OTA) in raw flour samples. This work highlights the potential of these beads as versatile tools for flow cytometry-based immunoassays, with significant implications for food safety, animal health, environmental monitoring, and clinical diagnostics.