Following article presents an efficient method for the core-shell systems preparation, composed of magnetic nanoparticles modified with molecularly imprinted polymers (mag-MIP). Obtained mag-MIP were utilized for pre-concentration and trace analysis of organic compounds in real samples. Superparamagnetic iron oxide nanoparticles (SPION) modified with TEOS (tetraethoxysilane) and MPS (3-(Trimethoxysilyl)propyl methacrylate) were used as the magnetic core, EGDMA (ethylene glycol dimethacrylate) was used as a cross-linking agent and AIBN (2,2′-azobisisobutyronitrile) as a thermal polymerisation initiator. Quercetin, estrone and β-estradiol were used as templates for which the appropriate monomers were chosen. Mag-MIP were successfully applied for the determination of chemical compounds in environmental samples. Quercetin, estrone and β-estradiol were adsorbed from their solutions onto the surface of functionalised SPION. Subsequently, mag-MIP were attracted by magnets immersed in the solutions and analysed via electrospray ionization mass spectrometry (ESI-MS) and flowing atmospheric pressure afterglow mass spectrometry (FAPA-MS) combined with thermally initiated desorption. The desorption occurs concomitantly with the plasma stream ioniaztion of the molecules, which are then transported to the analyser. FAPA-MS combined with mag-MIP is a novel analytical method suitable for trace detection from highly heterogeneous solutions. The combination of analyte pre-concentration with mag-MIP followed by FAPA-MS analysis significantly reduced limit of detection (LOD) for several trace analyses.