In the last two decades, metal-organic frameworks (MOFs) with highly tunable structure and porosity, have emerged as drug nanocarriers in the biomedical field. In particular, nanoscaled MOFs (nanoMOFs) have been widely investigated because of their potential biocompatibility, high drug loadings, and progressive release. To enhance their properties, MOFs have been combined with magnetic nanoparticles (MNPs) to form magnetic nanocomposites (MNP@MOF) with additional functionalities. Due to the magnetic properties of the MNPs, their presence in the nanosystems enables potential combinatorial magnetic targeted therapy and diagnosis. In this Review, we analyze the four main synthetic strategies currently employed for the fabrication of MNP@MOF nanocomposites, namely, mixing, formation of MNPs in presynthesized MOF, formation of MOFs in the presence of MNPs, and layer-by-layer methods. Additionally, we discuss the current progress in bioapplications, focusing on drug delivery systems (DDSs), magnetic resonance imaging (MRI), magnetic hyperthermia (MHT), and theragnostic systems. Overall, we provide a comprehensive overview of the recent advances in the development and bioapplications of MNP@MOF nanocomposites, highlighting their potential for future biomedical applications with a critical analysis of the challenges and limitations of these nanocomposites in terms of their synthesis, characterization, biocompatibility, and applicability.