This study aims at the possibility of single structured paramagnetic microparticles (PMPs), composed of maghemite (γ-Fe2O3) core modified with chitosan called MAN8, or tetraethyl orthosilicate covered with Dowex called MAN35, to be helpful for isolation of biogenic amines prior to their further analysis. Primarily, we synthesized and characterized PMPs. To obtain the information about bead morphology, scanning electron microscopy was employed. Furthermore, X-ray fluorescence was employed to carry out the elemental composition analyses. To obtain further insight into interaction between PMP surface and biogenic amines, scanning electron microscope was employed. It was shown that binding of biogenic amines causes increase of relative current response of deprotonated microparticles. We tested the specificity of PMPs to bind biogenic amines on histamine, tyramine, spermine, spermidine, putrescine, and cadaverine. We found that two types of our PMPs were able to selectively bind spermidine, cadaverine, and histamine in the case of MAN35; and histamine, tyramine, and putrescine in the case of MAN8. Finally, we carried out the analyses of real samples obtained from patients suffering from prostate carcinoma, where histamine was determined as the most abundant biogenic amine (10.456–13.654 µg mL−1). The prepared PMPs were able to isolate the biogenic amines from real samples, and thus they may be helpful in construction of biosensors, or Lab-on-a-Chip platforms, enabling less painful, and more rapid diagnosis of prostate cancer.