Earthworms are commonly known as essential modifiers of soil carbon (C) and nitrogen (N) cycles, but the effects of their species on nutrient cycles and interaction with soil microbial activities during the decomposition of organic materials remain unclear. We conducted an incubation experiment to investigate the effect of two different epigeic earthworms (M. hilgendorfi and E. fetida) on C and N concentrations and related enzyme activities in agricultural soils with added barley residues (ground barley powder). To achieve this, four treatments were included; (1) M. hilgendorfi and barley, (2) E. fetida and barley, (3) barley without earthworms, and (4) without earthworms and without barley. After 32 days incubation, we measured soil pH, inorganic N, microbial biomass C (MBC), water or hot-water soluble C, and soil enzyme activities. We also measured CO2 emissions during the incubation. Our results indicated the earthworm activity in soils had no effect on the cumulative CO2 emissions. However, M. hilgendorfi had a potential to accumulate MBC (2.9 g kg −1 soil) and nitrate-N (39 mg kg −1 soil), compared to E. fetida (2.5 g kg −1 soil and 14 mg kg −1 soil, respectively). In conclusion, the interaction between soil microbes and earthworm is influenced by earthworm species, consequently influencing the soil C and N dynamics.