The silvopastoral system avoids the degradation of tropical grasslands by providing essential nutrients to the soil while improving livestock diet and farmer's income by increasing the marketable wood supply. We hypothesize that intercropping shrub‐tree legumes into signalgrass increases microbial activity and soil organic matter (SOM) quality. We investigated silvopastoral system soils over 5 yr in a subhumid climate in northeastern Brazil to determine the total C and N contents and to estimate C‐microbial biomass and respiration, microbial and metabolic quotients, humic acid (HA), and fulvic acid (FA). The experimental design evaluated (a) signalgrass intercropped with gliricidia at 0, 4, and 8 m from the center of the double legume row; (b) signalgrass intercropped with sabia at 0, 4, and 8 m from the center of the double legume row; and (c) single signalgrass. Samples were obtained after 2, 3, 4, and 5 yr from silvopastoral system implementation. The shrub‐tree legumes soils had total C (39 g kg−1) and total N (3.8 g kg−1) contents significantly higher (30 and 72%, respectively) than single signalgrass soil only on the fifth year after establishment. Microbial biomass C at 0 and 4 m from the legume's rows was 700 mg kg−1, which was 75% higher than single signalgrass soils. There was strong microbial respiration (∼50 mg C‐CO2 kg−1 d−1) in legumes soils, but the metabolic quotient did not indicate disturbance in microbial activity. The microbial quotients were significantly higher in shrub‐tree legumes soil, and the HA/FA ratio was nearly 1, demonstrating greater efficiency in SOM decomposition by microbial activity. Overall, 5 yr after establishment, the silvopastoral system has improved SOM quality and contributed to grassland sustainability.