Earthworms can enhance plant productivity by promoting nitrogen (N) mineralization in N-limited agroecosystems and may also enhance the risk of N2O emissions and NO3−–N leaching in N-enriched agroecosystems. However, direct evidence demonstrating the enhancement by earthworms of N2O emissions and NO3−–N leaching in the field is scarce, particularly in intensively managed systems. In addition, the interaction of earthworm feeding strategies and organic amendment may profoundly modulate N cycling. We examined these impacts using two earthworm species with distinct ecological strategies (epigeic Eisenia foetida and endogeic Metaphire guillemi) in combination with two manure application methods (surface mulch and incorporation into the soil) in a field experiment. Our results demonstrated that earthworm addition significantly increased the crop yield by 18%–47% and cumulative N2O emissions by 19%–25% largely regardless of earthworm species and manure application methods, respectively. However, earthworms did not significantly increase the leachate NO3−–N concentration. Earthworm-induced N2O emissions were primarily attributed to increased soil N availability (NO3−–N and microbial biomass N) and carbon (C) availability (dissolved organic C). In contrast, a stepwise regression revealed that an earthworm-promoted soil macroaggregation exerted negative effects on N2O emissions. Irrespective of earthworm species and manure application methods, earthworms had no stimulatory effects on the yield-scaled N2O–N because the promotion of crop productivity counteracted the extent of N2O increase. In conclusion, understanding the trade-off between earthworm services and dis-services will contribute to the development of environmentally justified soil management by allowing the full utilization of biological resources.