Background and aims <p>Green manuring offers an effective approach to improve soil health and crop yield. However, the potential effects of green manuring on fruit quality and the underlying mechanisms have not been ascertained. This study investigated green manure-mediated metabolic changes in strawberry (<i>Fragaria</i> × <i>ananassa</i> Duch.) fruit quality and their relationship to the reshaping of rhizosphere microbiome.</p> Methods <p>Fresh maize straw was ploughed into the soil at a rate of 20,000 kg ha^–1 three weeks before transplanting strawberry. The global changes in fruit quality were analyzed by widely targeted metabolomics and transcriptomics. Rhizosphere bacterial and fungal communities were characterized based on amplicon sequencing.</p> Results <p>Green manuring with maize enhances fruit flavor, color, and functional quality, as indicated by increased accumulation of soluble sugars, flavonoids, and bioactive compounds. The changes in fruit metabolite composition are consistent with transcriptional upregulation of functional genes in specific metabolic pathways. Rhizosphere microbial communities show higher diversity and network complexity under green manuring, with more potentially beneficial bacteria and fewer pathogenic fungi.</p> Conclusions <p>The results uncover strong cross-kingdom interactions between strawberry plants and rhizosphere microbes mediated by green manure, which contributes to fruit quality through sophisticated metabolic reprogramming.</p>