<p>Metal–organic frameworks (MOFs) are highly versatile porous crystalline polymers with diverse structural compositions, high porosity, and biocompatibility, which guarantees their significant potential in various biomedical applications, including drug delivery, magnetic resonance imaging (MRI), and biosensing. However, despite these promising features, MOFs’ application is considerably hindered by main challenges such as toxicity and biocompatibility. This review aims to provide a comprehensive understanding of MOF-associated toxicity, and the challenges involved in their biomedical applications. We first addressed the different routes of MOFs exposure, such as oral ingestion, inhalation, skin, and intravenous routes, and their potential contribution to MOF-associated toxicity. Further, we focused on drug delivery systems, MRI contrast agents, and biosensors, along with their key challenges, like how toxicity issues affect their efficacy and safety. The key biological mechanisms involved in MOF-induced toxicity were also critically examined, such as oxidative stress, mitochondrial dysfunction, and autophagy disruption. Moreover, we evaluated how MOFs’ toxicity prolife is influenced by their physicochemical properties such as MOFs’ composition, size and shape, surface characteristics, biodegradability, and stability. The current advancements were also illustrated to address these challenges and to minimize the toxicity with enhancement in therapeutic performance, such as the development of stimuli-responsive drug delivery systems and MOF-based composites with better biocompatibility and efficacy. Overall, this review enlightens the need for novel strategies to overcome the current challenges in MOFs’ biomedical applications. Future research should focus on the evaluation of systematic toxicity and development of novel, suitable MOF-based composites to ensure their safety and efficacy.</p> Graphical Abstract <p></p>