Self-assembled core–shell Ni–C nanoparticles (NPs) with nearly uniform sizes were grown on the van der Waals (0001) surfaces of GaSe layered crystals. The metal NPs encapsulated within graphite shells (Ni@C) with the sizes ranging from a few to 15 nm were produced by electron beam induced vacuum deposition from metal-carbon melts under UV-irradiation without annealing after the deposition. The samples were characterized by X-ray diffraction, atomic force microscopy, X-ray photoelectron spectroscopy, Raman spectroscopy. The van der Waals interactions between the NPs and the surface electrostatic interactions are utilized for encapsulated NPs self-assembly. The Coulomb staircases and the negative differential conductance were observed at temperatures lower than 300 K in the current–voltage (I–V) curves of the vertical hybrid structures Au/Ni/(Ni–C)/Ni@CNCs/n-Ga2O3/p-GaSe/In consisting of ferromagnetic metal Ni, (Ni–C) nanocomposite thin film and two layers of magnetic NPs (Ni@CNCs), which were embedded in n-Ga2O3 wide-band-gap oxide. The I–V characteristics of this structure depend on orientation of the external weak (∼60 mT) magnetic field relative to the (0001) GaSe plane. Peculiarities observed in the I–V characteristics of the hybrid structures may be caused by magnetic-field-dependent phenomena of spin-dependent tunneling through the barriers, which gives rise to spin accumulation, and spin-polarized electric current interactions with magnetic NPs.