Ensuring food quality and safety is a cornerstone of modern agriculture, encompassing all stages of production, processing, storage, and distribution. Agricultural products are vulnerable to contamination by various harmful substances, including mycotoxins such as ochratoxin A, zearalenone, and aflatoxin B1. These toxic compounds are produced by certain fungi and pose serious health risks to humans and animals. Developing efficient methods for optimizing detection systems is crucial for addressing contamination challenges. This study focuses on creating an optimized methodology for the development of magnetic immunochromatographic assays for the detection of these mycotoxins in cereal products. This study employed spherical superparamagnetic nanoparticles as a basis for the immunochromatographic assay. A competitive immunoassay format was used as the foundation for quantifying the studied mycotoxins in cereal samples. The methodology included the covalent immobilization of antibodies specific to each mycotoxin on the surface of magnetic nanoparticles. Antigen-coated conjugate pads were prepared for each mycotoxin to serve as test lines. The systematic optimization of parameters such as the density of antibodies on magnetic particles, the amount of bioconjugates used in each test, and the antigen printing density on the test lines was performed. Quantitative measurements of the magnetic nanoconjugates’ distribution were carried out using the magnetic particle quantification method. The optimized parameters were validated against high-performance liquid chromatography (HPLC) results for cereal products contaminated with the studied mycotoxins. The developed methodology enabled the systematic optimization of key assay parameters to achieve high sensitivity and specificity for detecting the studied mycotoxins. Adjustments to the density of antibodies immobilized on magnetic nanoparticles were made within a range of 0.25 to 7.5 µg per conjugation. Optimal conditions were identified by achieving the maximum signal-to-noise ratio at a toxin concentration of 1 ng/mL. The additional fine-tuning of bioconjugate amounts and antigen printing densities ensured reproducibility and sensitivity. The validation process demonstrated that assays developed using this methodology achieved detection limits in the low ng/mL range and showed excellent correlation with HPLC data. The proposed methodology provides a robust framework for optimizing magnetic immunochromatographic assays for the detection of mycotoxins in cereal products. This approach enables the efficient development of reliable test systems, contributing to enhanced food safety and quality assurance across the agricultural supply chain.