Multidrug and toxic compound extrusion (MATE) transporters play critical roles in plant stress responses, including heavy metal detoxification. Although manganese (Mn) toxicity severely limits crop productivity worldwide, the involvement of MATE transporters in Mn tolerance remains poorly understood, especially in perennial fruit crops. In this study, we identified 65 MATE genes in Prunus persica genome, phylogenetically classified into four distinct clades. Gene duplication analysis revealed that the expansion of the PpMATE family is driven by both tandem and segmental events. Transcriptional profiling under Mn stress identified PpMATE49 as a highly responsive transporter. Subcellular localization confirmed its plasma membrane presence, and heterologous expression in yeast demonstrated its functional role in alleviating Mn-induced growth arrest and reducing intracellular Mn levels. Further functional validation showed that PpMATE49 overexpression in tobacco and peach leaves significantly reduced Mn accumulation and enhanced Mn tolerance, whereas its silencing in peach seedlings led to Mn hyperaccumulation and exacerbated toxicity. Notably, PpMATE49 overexpression in peach roots promoted root growth, reduced Mn accumulation, and improved plant tolerance under Mn stress. Our results establish PpMATE49 as a key mediator of Mn detoxification in peach and offer a promising genetic target for improving Mn tolerance in fruit crops.