Management intensive grazing (MIG), also known as rotational grazing or multi-paddock grazing, is purported to sequester carbon (C) in soils compared to other agricultural management systems. Prior research examining the potential for MIG to enhance soil C has been inconclusive, and past investigations have not addressed whether higher nitrous oxide (N2O) emissions may accompany increases in soil C stocks. Here we examined linkages among MIG, soil C accumulation, and N2O emissions in cool-season, organic pastures of the northeastern United States. We found that pastures under MIG increased soil C concentrations by 11% from 0–15 cm depth but that soil C stocks at all sampled depths did not differ between hayed and grazed fields. We observed a divergent response in soil N to MIG, where both N concentrations and stocks significantly increased and the soil C:N ratio significantly decreased in rotationally grazed pastures. Our results also demonstrated that during the second year of the study, N2O emissions were on average 33% higher in grazed fields and compared to hayed fields. These elevated N2O fluxes in MIG fields may have offset any soil C gains achieved under MIG, as demonstrated by similar climate forcing values (as CO2-equivalents) for hayed and grazed pastures over a 100-year time horizon. The significant variation we detected among farms in soil C and N stocks, soil microbial activity, plant biomass production, and soil greenhouse gas emissions demonstrates that MIG does not have uniform effects across the landscape. Overall, our study demonstrates that care should be taken when promoting management practices that may have unintended climate consequences.