Soil fertility in sub-Saharan Africa is often degraded by poor farming. Microorganisms are essential to nutrient cycling and soil health, yet traditional methods often overlook their complexity. This study assessed the impact of land management on microbial diversity, enzyme activity, and nutrient availability in cashew-based agroforestry systems in Benin. Three integrated systems S1 (Sorghum bicolor–cattle), S2 (S. bicolor–cashew at low and high densities), and S3 (S. bicolor–cashew–cattle) were compared to a conventional monocrop (CFS). A randomized block design across four villages in Tchaourou yielded 72 soil samples, analyzed for microbial biomass carbon (MBC), enzyme activities (urease, dehydrogenase, phosphatase), and microbial populations. The results indicated that dehydrogenase activity increased from 16.59 to 56.46 μg TPF (triphenyl formazan) g⁻¹ soil (S2-HD to S3-LD; +240%). Phosphatase activity rose from 388.25 to 771.29 μmol PNP (p-nitrophenol) g⁻¹ soil (+99%). In contrast, CFS showed a decrease in dehydrogenase from 16.63 to 15.89 (-4.4%) and a slight increase in phosphatase from 299.21 to 312.58 (+4.5%). Urease activity peaked at 882.45 μmol NH₄⁺/g·h in S3-LD, a 239% increase over CFS, which declined from 317.54 to 260.23 μmol NH₄⁺/g·h (-18.1%) in the second year. MBC increased from 679.45 to 2,289.29 µg C/g soil (+237%) in integrated systems, while it decreased from 789.25 to 761.23 µg C/g soil (-3.5%) in CFS. SBR (soil basal respiration) improved from 4.02 to 6.71 mg C-CO₂/kg·h in integrated systems (+67%), while it rose modestly from 4.01 to 4.62 (+15.2%) in CFS. S3-LD consistently outperformed the other systems, highlighting the benefits of integrated farming for soil health. This system showed the highest levels of enzymatic activity, microbial biomass, and respiration, suggesting a more active and diverse microbial community that enhances nutrient cycling and fertility. Overall, integrated farming improved soil quality more than conventional farming, supporting productivity and ecosystem function.