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Background: Reports on the mycotoxin ochratoxin A occurrence in wine and beer indicate that this is a worldwide problem due to the widespread consumption of these beverages. Objective: The existing solid phase extraction methods for the ochratoxin A are usually used in the form of microcolumns, which are generally driven by pumps and take a long time to finish sample pretreatment. It is highly desirable to develop fast, reliable, and low-cost analytical procedures for the monitoring of ochratoxin A in wine and beer. Method: A method comprising magnetic solid-phase extraction (MSPE) followed by high-performance liquid chromatography with fluorescence detection (HPLC-FLD) was developed for the quantification of ochratoxin A in wine and beer. Hexadecyl-immobilized silica-coated magnetic Fe3O4 (C16- Fe3O4@SiO2) nanoparticles were prepared by single-step sol-gel modification of bare Fe3O4 nanoparticles and were used as MSPE adsorbents. Results: Key parameters that affect the MSPE of ochratoxin A in wine and beer, namely, the pH, content of organic components, and desorption solution, were investigated in detail. Under the optimized extraction conditions with gradient chromatographic separation, a limit of detection of 0.02 μg L-1, a precision of 4.4%, and recoveries in the range of 89.7–103.6% were achieved for the determination of ochratoxin A in wine and beer. Conclusion: A MSPE method using C16-Fe3O4@SiO2 nanoparticles as the adsorbent in combination with HPLC-FLD was developed for the determination of ochratoxin A in wine and beer. The validated method is able to provide reliable date at the lower level, displaying satisfactory linearity, precision, accuracy and moderate cost.