This study investigates how different crop combinations influence the interaction between peanut plants and their rhizosphere microbiota through metabolite deposition and functional responses of free-living and symbiotic nitrogen-fixing bacteria. Over an 8-year period, a field experiment comparing peanut monoculture, peanut-oilseed rape rotation, and peanut-maize intercropping with oilseed rape showed that crop diversification significantly enhanced peanut performance, root nodulation, and free-living nitrogen fixation. The most diverse system (peanut-maize intercropping with oilseed rape) increased peanut height, biomass, and fruit weight by 19%, 66%, and 46%, respectively, compared to peanut monoculture and peanut-oilseed rape rotation. These improvements were associated with higher nitrogen uptake and increased root nodulation, with a threefold higher nodule density and sixfold higher nodule-to-root mass ratio in the crop mixture. Chemical analysis revealed that specific metabolites, such as flavonoids and coumarins, accumulated in the peanut rhizosphere due to the activation of phenylpropanoid biosynthesis pathways. These metabolites enhanced the growth and nitrogen fixation activity of free-living bacterial isolates and root nodulation by symbiotic *Bradyrhizobium* isolates. The study demonstrates that tailored intercropping can improve soil nitrogen availability through changes in the rhizosphere microbiome and its functions, highlighting the importance of chemical signaling between plants and soil microbiota in sustainable crop production.This study investigates how different crop combinations influence the interaction between peanut plants and their rhizosphere microbiota through metabolite deposition and functional responses of free-living and symbiotic nitrogen-fixing bacteria. Over an 8-year period, a field experiment comparing peanut monoculture, peanut-oilseed rape rotation, and peanut-maize intercropping with oilseed rape showed that crop diversification significantly enhanced peanut performance, root nodulation, and free-living nitrogen fixation. The most diverse system (peanut-maize intercropping with oilseed rape) increased peanut height, biomass, and fruit weight by 19%, 66%, and 46%, respectively, compared to peanut monoculture and peanut-oilseed rape rotation. These improvements were associated with higher nitrogen uptake and increased root nodulation, with a threefold higher nodule density and sixfold higher nodule-to-root mass ratio in the crop mixture. Chemical analysis revealed that specific metabolites, such as flavonoids and coumarins, accumulated in the peanut rhizosphere due to the activation of phenylpropanoid biosynthesis pathways. These metabolites enhanced the growth and nitrogen fixation activity of free-living bacterial isolates and root nodulation by symbiotic *Bradyrhizobium* isolates. The study demonstrates that tailored intercropping can improve soil nitrogen availability through changes in the rhizosphere microbiome and its functions, highlighting the importance of chemical signaling between plants and soil microbiota in sustainable crop production.