Iron (Fe) deficiency restricts crop yields in calcareous soil. Thus, a novel Fe chelator, proline-2′-deoxymugineic acid (PDMA), based on the natural phytosiderophore 2′-deoxymugineic acid (DMA), was developed to solve the Fe deficiency problem. However, the effects and mechanisms of PDMA relevant to the Fe nutrition and yield of dicots grown under field conditions require further exploration. In this study, pot and field experiments with calcareous soil were conducted to investigate the effects of PDMA on the Fe nutrition and yield of peanuts. The results demonstrate that PDMA could dissolve insoluble Fe in the rhizosphere and up-regulate expression of the yellow stripe-like family gene AhYSL1 to improve the Fe nutrition of peanuts. Moreover, the chlorosis and growth inhibition induced by Fe deficiency were significantly diminished. Importantly, under field conditions, the peanut yield and kernel micronutrition were notably promoted by PDMA application. Our results indicate that PDMA promotes the dissolution of insoluble Fe and a rich supply of Fe in the rhizosphere, increasing yields through integrated improvements in soil–plant Fe nutrition at the molecular and ecological levels. In conclusion, the efficacy of PDMA for improving the Fe nutrition and yield of peanut indicates its outstanding potential for agricultural applications.