Piper nigrum–Areca catechu intercropping mitigates soil problems related to continuous P. nigrum cropping, but the exact reason for this is not clear. In this study, the intercropping system increased P. nigrum’s single plant weight by 27.0–55.5% and unit yield per hectare by 5.1–33.5% in 2019–2022. Intercropping altered the metabolic profiles of root exudates from both species, with increases in flavonoids (epicatechin and 4′,5,6,7-Tetramethoxyflavone), alkaloids (litebamine), and amino acids (proline betaine, L-homocysteic acid and L-homocysteic acid). Intercropping further increased the abundance of dominant soil bacteria, including GAL15 (354.9%) and Bacteroidota (70.4%) in the P. nigrum rhizosphere, and Firmicutes (141.8%) and WPS2 (75.3%) in the A. catechu rhizosphere. In the intercropping system, the abundance of soil flavonoids, including tangeritin, trifolirhizin, and hexamethylquercetagetin, which participated in improving nutrient absorption and plant growth, increased by 106.4~356.0%, 28.9~45.5%, and 45.2~127.1%, respectively, during the whole growing period. Overall, intercropping with A. catechu promoted carbon input to the P. nigrum soil via root exudates. This increased the diversity of P. nigrum rhizosphere beneficial bacterial communities, as well as the amounts of nutrients and plant growth-promoting secondary metabolites. Together, these effects improved nutrient uptake and utilization, thereby driving the sustainable production of P. nigrum, and ultimately achieving higher yields.