Zearalenone (ZEN) is a nonsteroidal estrogenic mycotoxin produced by various Fusarium species and commonly occurring in corn and other cereals. Even though its acute toxicity is low, still the estrogenic activity of ZEN and metabolites is a matter of concern. In this work, a new magnetic molecularly imprinted polymer (mMIP) for the selective extraction of ZEN from cereal flours is presented. The mMIP was synthesized previously using quercetin as dummy template, and here we wanted to test its applicability to complex food samples. Analyte determination was carried out by high-performance liquid chromatography coupled to tandem mass spectrometry. The selectivity of the mMIP and the main validation method parameters were assessed. In particular, even in samples as complex as cereals, matrix effect was negligible. Although the mMIP showed cross-selectivity towards both ZEN-related and quercetin-related compounds, nonetheless ZEN recovery was > 95% for the two lower spiking levels, and the quantification limit was 0.14 ng g⁻¹, i.e., ca. 500 times lower than the maximum limit fixed for most cereals by European law. Therefore, the material, also in comparison with a commercial sorbent, appears suitable for the application in food analysis, also to isolate ZEN at trace levels.