Despite early clinical success, the mechanisms of action of low-dose interleukin-2 (LD-IL-2) immunotherapy remain only partly understood. Here, we examine the effects of interval administration of low-dose recombinant IL-2 (iLD-IL-2) using high-resolution, single-cell multiomics. We confirmed that iLD-IL-2 selectively expands thymic-derived FOXP3+HELIOS+ Tregs and CD56br NK cells, and provide new evidence for an IL-2-induced reduction of highly differentiated IL-21-producing CD4+ T cells. We also discovered that iLD-IL-2 induces an anti-inflammatory gene expression signature, which was detected in all T and NK cell subsets even one month after treatment. The same signature was present in COVID-19 patients, but in the opposite direction. These findings indicate that the sustained Treg and CD56br NK cell increases induced by our 4-week iLD-IL2 treatment create a long-lasting and global anti-inflammatory environment, warranting further investigations of the potential clinical benefits of iLD-IL-2 in immunotherapy, including the possibility of reversing the pro-inflammatory environment in COVID-19 patients.