Aims <p>With the rapid expansion of peach cultivation in China, a substantial amount of pruned peach branch waste is generated annually. However, research on the sustainable disposal of these branch waste remains limited. This study aims to evaluate the potential of returning discarded peach branches to the field as a novel approach for resource recycling.</p> Methods <p>We evaluated the effects of three field return methods—organic fertilizer (OF), mushroom substrate (PM) and surface covering (SC)—on soil physicochemical properties. Metagenomic analysis was employed to investigate the impact of these treatments on soil microbial communities and nitrogen cycling-related genes.</p> Results <p>All return methods significantly increased soil nutrient content, microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN). Metagenomic analysis revealed that these treatments markedly altered the composition, diversity and abundance of nitrogen cycling-related functional genes in soil microbial communities. Notably, surface covering (SC) significantly enhanced the abundance of nitrogen fixation genes (<i>nifH</i>, <i>nifD</i> and <i>nifK</i>) and nitrification-related genes (<i>hao</i>, <i>hcp</i> and <i>nirS</i>) and promoted the enrichment of nitrogen-fixing microbes such as Methylocaldum and Anaeromyxobacter. Moreover, changes in nitrogen cycling genes were strongly correlated with total carbon (TC), available potassium (AK), MBC and MBN.</p> Conclusions <p>Our findings suggest that surface covering is an effective method for the field return of peach branch waste, capable of improving soil quality, enhancing nitrogen availability, optimizing microbial nitrogen cycling functions and promoting overall soil health.</p> Graphical Abstract <p></p>