In this paper, the investigations were carried out to reveal the complex nature of the nanocrystalline magnetic cores and to validate the hypothesis that magnetic molecularly imprinted polymer (MMIP) could be used as an effective sorbent during analysis of biomolecules but the adsorbate-sorbent process is independent from the amount of siloxane functionalized magnetite core (Fe3O4@SiO2-MPS). For that purpose, molecularly imprinted shell layer composed from poly(methacrylic acid-co-ethylene glycol dimethacrylate) was conjugated to various amounts of Fe3O4@SiO2-MPS. Magnetic measurements showed single-domain-type magnetic behavior for all materials. Thermal decomposition process revealed different enthalpies (110 to 279 J g−1) with the highest value for MMIP prepared from the lowest amount of Fe3O4@SiO2-MPS. The morphological and structural analyses proved a presence of single magnetite crystallite and elemental mapping confirmed core–shell structure. The binding capacities for MMIPs revealed similar values (0.897 ± 0.114 to 1.019 ± 0.129 µg g−1) and specificity (IF: 3.36 to 3.99). The MMIP sorbent was used to determine model biomolecule of tyramine in wine in the validated analytical method, proving the stability of sorbent. The lower tyramine levels were found in Chilean and Australian wines (0.42 ± 0.03 and 0.15 ± 0.01 mg L-1, respectively) and higher in French one (7.58 ± 0.15 mg L-1).