Agroforestry systems are considered promising alternatives to rubber tree (Hevea brasiliensis) monocultures, but information is limited on the effects of rubber-based agroforestry systems on soil organic carbon (SOC) and total nitrogen (TN) storage. The current study, which was conducted in Xishuangbanna, China, compared four intercropping treatments, including rubber monoculture and the follow three agroforestry treatments: intercropping with Camellia sinensis, Coffea liberica, or Theobroma cacao. Soil physicochemical properties and copy numbers of cbbL and nosZ genes (which indicate the abundance of bacteria that function in C and N cycling) were analyzed. The results showed that Coffea liberica intercropping facilitated SOC and TN contents and enhanced SOC and TN stocks by 36.5 and 33.2% relative to rubber monoculture at 0-10 cm soil layer, respectively. Structural equation modeling showed that the effects of intercropping on cbbL and nosZ copy numbers were mainly explained by soil pH and bulk density (r 2 = .37 and .35, respectively), that the abundance of cbbL and SOC content directly affected SOC storage (r 2 = .46), and that the abundance of nosZ and TN content directly affected TN storage (r 2 = .22). Our results indicate that the use of C. liberica as intercrops should contribute to retard soil degradation and to implement sustainable land management in rubber monocultures. Combining the abiotic and microbial pathways, we suggest that the enhancement of C and N sequestration with C. liberica under rubber monoculture can be probably attributed to the increased input of litter and roots and to the stimulation of the microorganisms that regulate C and N cycles.