Tetrabromobisphenol A (TBBPA) is a flame retardant widely added to polymer products. Successful isolation of target analytes from complex natural matrices relies on extraction materials that can selectively interact with the analytes. In this context, the use of magnetic nanostructured adsorbents, such as magnetic molecularly imprinted polymer systems (MMIPs), can play a key role in both selective matrix–analyte interactions and separation processes. Here, to achieve different TBBPA loadings, Fe₃O₄ nanoparticles (NPs) were coated with chitosan (CS) or (3-aminopropyl) triethoxysilane (APTES). Moreover, to further promote template–NP interactions and modulate the polymeric shell thickness of MMIPs, 3,4-dihydroxyhydrocinnamic acid (HC) was covalently bonded in different amounts to APTES-functionalized MNPs. Thermal, SEM, and elemental analyses showed a different coating degree of the nanocomposites (Fe₃O₄@CS-MIP size d = 77 nm and Fe₃O₄@APTES-MIP d = 20 nm). In addition, it was confirmed that the adsorption mechanism of TBBPA on Fe₃O₄@APTES-HCX-MIPs was due to specific interactions between the systems and the analyte, unlike non-imprinted analogs (MNIPs). Among the developed systems, the Fe3O4@APTES-HC0.7-MIP sample showed the best extraction efficiency (85%) associated with good discharge efficiency (70%). Furthermore, this nanocomposite displayed high selectivity towards TBBPA (ε > 1) and good extraction efficiency in three consecutive cycles (67%), demonstrating great potential in the environmental field.