Intercropping of quinoa with legumes has been studied infrequently, despite quinoa’s global importance as a nutrient-dense crop with resilience to diverse growing conditions. This study aims to elucidate the benefits of intercropping by comparing quinoa monocropping with intercropping with red bean, mung bean, and black bean, focusing on yield, plant nutrients, and soil physicochemical properties. The land equivalent ratio of quinoa/legumes intercropping consistently exceeded 1, peaking at 1.52 for quinoa/red bean intercropping, indicating higher productivity than monocropping. Quinoa/red bean intercropping increased the nutrient contents of quinoa plants throughout the quinoa growth period and exhibited the highest levels of ammonium nitrogen, available phosphorus, available potassium, and organic matter content, alongside the highest activity of sucrase, alkaline phosphatase, and urease enzymes in the soil during the quinoa seedling stage. At maturity, quinoa/mung bean demonstrated the highest levels of available phosphorus and total nitrogen, while quinoa/red bean displayed the highest sucrase and urease enzyme activity. Significantly positive correlations were found between the nitrogen, phosphorus, and potassium contents of quinoa and most soil nutrients. Regression analysis revealed a positive relationship between soil phosphatase activity and quinoa yield. Intercropping quinoa with legumes improved yield, plant nutrients, soil nutrients, and soil enzyme activity, with quinoa/red bean exhibiting the most remarkable effect.