Magnetic nanocomposites (MNCs) combine the features of magnetic nanoparticles and a second material, which provide distinct physical, chemical, and biological properties. The magnetic core for nanocomposite synthesis is extensively used due to its high saturation magnetization, chemical stability, large surface area, and easy functionalization. Moreover, magnetic nanoparticles (MNPs) have great potential for magnetic resonance imaging (MRI), magnetic particle imaging (MPI), hyperthermia, and targeted drug and gene delivery by an external magnetic field. Numerous composing units exist, which leads to the outstanding application of composites. This review focuses on nucleic acid-based bioapplications of MNCs with polymeric, organic, inorganic, biomolecules, and bioinspared surface coating. In addition, different forms, such as core–shell, doping, multilayer, yolk–shell, and Janus-shaped hybrids, are discussed, and their unique properties are highlighted. The unique types of nanocomposites as magnetic molecularly imprinted polymer (MMIP) properties are presented. This review presents only the synthesis of MNCs using ready-made magnetic cores. These restrictions are associated with many materials, the quantitative and qualitative magnetic core composition, and synthesis procedures. This review aims to discuss the features of nucleic acid-based MNC information available to researchers in this field and guide them through some problems in the area, structure variation, and surface functionalization possibilities. The most recent advancements of MNCs and imprinted polymers in nucleic acid-based therapy, diagnostics, theranostics, magnetic separation, biocatalytic, and biosensing are introduced.