Myeloid cell functional reprogramming represents a compelling therapeutic approach to induce immunological tolerance, but remains unexplored clinically. We developed a short-term nanoimmunotherapy, based on mammalian target of rapamycin (mTOR) involving drug-loaded high-density lipoprotein (HDL) nanoparticles that target macrophages and prevent epigenetic modifications associated with trained immunity. Using an experimental heart transplantation mouse model, we found that inhibition of aerobic glycolysis in myeloid cells through systemic administration of mTOR-specific nanoimmunotherapy (mTORi-HDL) prevents macrophages’ trained immunity phenotype and induces accumulation of regulatory macrophages. Remarkably, short-term mTORi-HDL treatment in combination with an inhibitory CD40- TRAF6 specific nanoimmunotherapy (TRAF6i-HDL) resulted in indefinite allograft survival. Together, these findings demonstrate that HDL-based nanoimmunotherapy provides an innovative approach to control macrophage function in vivo and promote immunological tolerance.