In a changing climate, extreme weather events are predicted to increase in frequency and magnitude. These events may induce stress in plants and soil microbial communities, but the impact of climate extremes on root-soil interactions remains poorly understood. To better understand the response of a temperate agroecosystem to winter freezing and drought, a mild (−5 °C) or severe (−10 °C) freeze-thaw, or dry-wet cycle was imposed on mesocosms planted with winter wheat (Triticum aestivum L.) and unplanted soil. We measured the effect of the stresses on greenhouse gas (GHG) fluxes (CO2, N2O, CH4), plant tissue composition, soil solute concentrations and soil microbial community structure. Only the most severe freezing event had a direct effect on soils, with pulses of CO2 and N2O released after thawing. In contrast, all stresses reduced C fixation and respiration in planted treatments. Total CO2 flux from planted mesocosms was reduced during the drought period and CO2 flux was negatively correlated with soil water content. The severe freeze-thaw event caused lasting damage to plants and increased rhizodeposition, resulting in increased CO2 efflux and a small alteration in soil microbial community composition. The presence of plants resulted in significantly greater total CO2 flux following freeze-thaw or dry-wet events, but only in unplanted soil was there a net increase in GHG emissions. These results demonstrate that, although the effects of stress appear magnified where plants are present, the maintenance of winter plant cover in temperate agricultural soils reduces the effects of extreme weather events on future climate.