Pyrroloquinoline quinone (PQQ) is a bioactive compound that has attracted significant attention due to its potential health benefits. In this study, we developed a new magnetic molecularly imprinted nanoparticle (MMIN) for the selective extraction and determination of PQQ from food samples. The MMIN was synthesized using a surface molecular imprinting technique with PQQ as the template molecule, Fe3O4 nanoparticles as the magnetic core, and methacrylic acid as the functional monomer. The MMIN exhibited high selectivity and affinity towards PQQ, allowing for efficient extraction and preconcentration of PQQ from complex food matrices. The extracted PQQ was then quantified using HPLC-DAD. The developed method showed good linearity (R2 = 0.9985) and low limits of detection (0.03 μg L-1). The accuracy and precision of the method were evaluated by analyzing spiked food samples, with average recoveries close to 89.8%. The MMIN also demonstrated good reusability, with negligible decrease in extraction efficiency after five cycles of use. Overall, the developed MMIN-based method provides a reliable and efficient approach for the analysis of PQQ in food samples.