The melon/cowpea intercropping system can be a specific and efficient cropping pattern in a horticultural field. Intercropping systems contribute to the optimization of land use, fostering sustainable and efficient agriculture. This study entails a first-year comparative intercropping assay using cowpea (Vigna unguiculata) and melon (Cucumis melo) under organic management with different patterns and 30% less organic fertilization than usual in monocrops. We determined the soil nutrients, physicochemical properties, enzyme activities and microbes by high-throughput sequencing. We found that the intercropping system changed the bacterial community structure independently of the intercropping pattern. The bacterial community was characterized by a higher abundance of the phyla Proteobacteria and Bacteroidetes phyla and of the genus Pseudomonas, which are related to nutrient cycling, and by greater amounts of other beneficial microorganisms like Bacillus, Streptomyces and Sphingomonas. The intercropped systems significantly boosted the total nitrogen, available phosphorus and total organic carbon levels in addition to the melon yield. They also enhanced the acid phosphatase and β-glucosidase activity compared to the melon monocrop. Results from this study suggest that melon/cowpea intercropping, starting from the first year, not only provides a stable supply of food and income due to the diversified cropping systems, but is also beneficial for the soil microbial community and environment.