In this work, the synthesis of molecularly imprinted polymer microspheres with narrow particle size distributions and core-shell morphology by a two-step precipitation polymerization procedure is described. Polydivinylbenzene (poly DVB-80) core particles were used as seed particles in the production of molecularly imprinted polymer shells by copolymerization of divinylbenzene-80 with methacrylic acid in the presence of thiabendazole (TBZ) and an appropriate porogen. Thereafter, polymer particles were packed into refillable stainless steel HPLC columns used in the development of an inline molecularly imprinted SPE method for the determination of TBZ in citrus fruits and orange juice samples. Under optimized chromatographic conditions, recoveries of TBZ within the range 81.1–106.4%, depending upon the sample, were obtained, with RSDs lower than 10%. This novel method permits the unequivocal determination of TBZ in the samples under study, according to the maximum residue levels allowed within Europe, in less than 20 min and without any need for a clean-up step in the analytical protocol.