Growers use cover crops to provide nutrients for crops and build soil organic matter (SOM). Termination methods may alter the effects of cover crops on soil labile C and N. We examined how two cover crops and three termination methods affected soil microbes, soil aggregates, and C and N pools in an organic grain system. We compared crimson clover (Trifolium incarnatum L.) (CC), hairy vetch (Vicia villosa Roth) (HV), and a control together with disking, mowing, or a roller-crimper for effects on hot-water-extractable carbohydrates, microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN), potentially mineralizable C and N, and aggregation (quantified by mean weight diameter [MWD]). Disking comprised flail mowing plots and then cultivating. Roller-crimping occurred via a roller with blades. Vetch soil contained 14% higher MBC than no cover crop pretermination, possibly because of enhanced rhizodeposition. Planting CC resulted in 44% higher MBC than no cover crop a week after termination, likely due to its higher biomass C/N ratio. Disking decreased MWD relative to flail mowing in no cover crop soils at 4 wk after termination across both years at 0-to-5-cm depth. In addition, MWD was lower under CC than under no cover crop for both the flail mowed and roller-crimped treatments at 4 wk after termination across both years from 0 to 5 cm. This is possibly due to enhanced desiccation of the soil in bare plots after termination. Our results indicate that quantity and quality of biomass of different legume species, rather than termination methods, dominated effects on labile C.