Magnetic nanocomposites involving tetraborate ion (TB)-intercalated Mg–Al-layered double hydroxide (LDH) shell supported on magnesium ferrite core particles are synthesized, characterized, and compared with their non-magnetic analogues. The compositions of the obtained nanocomposites were determined and structural investigations were made by powder X-ray diffraction and Fourier transform infrared spectroscopy. Particle characteristics were examined by size distribution, specific surface area measurements, scanning electron microscopy and transmission electron microscopy. Room-temperature magnetic measurements were performed with a vibrating sample magnetometer. The dynamics and structure of the interlayer water molecules and borate ions were studied by molecular dynamics simulations. Analytical and modeling studies verified that the TB ions were arranged between the LDH layers in oblique positions. The products were found to carry ca. 6% boron (1017 B atom/μg nanocomposite). The magnetic nanocomposite showed superparamagnetic properties and can potentially find applications in biomedical fields for the site-specific delivery of bio-potent boron agents.