Induced tolerogenic dendritic cells are a powerful immunotherapy for autoimmune disease that have shown promise in laboratory models of disease and early clinical trials. In contrast to conventional immunosuppressive treatments, tolerogenic immunotherapy leverages the cells and function of the immune system to quell the autoreactive lymphocytes responsible for damage and disease. The principle techniques of isolating and reprogramming dendritic cells (DCs), central to this approach, are well characterized. However, the broader application of this technology is limited by its high cost and bespoke nature. Nanomedicine offers an alternative route by performing this reprogramming process in situ. Here, we review the challenges and opportunities in using nanoparticles as a delivery mechanism to target DCs and induce immunomodulation, emphasizing their versatility. We then highlight their potential to solve critical problems in organ transplantation and increasingly prevalent autoimmune disorders such as type 1 diabetes mellitus and multiple sclerosis, where new immunotherapy approaches have begun to show promise. Tolerogenic dendritic cells inhibit inflammatory responses against self-antigens, offering a therapeutic strategy for autoimmune diseases. This Review describes the nanotechnology-based approaches available to target dendritic cells and induce tolerogenic properties, highlighting applications in organ transplantation, multiple sclerosis and diabetes mellitus.