The interest in bioenergy crops has raised questions as to the potential of management strategies to preserve soil C pools and soil quality. Since soil-surface CO₂ effluxes are a major fate of soil C, knowledge of CO₂ efflux’s spatial and temporal trends among bioenergy crops will facilitate advances in research on improving terrestrial C-cycle models as well as decision support tools for policy and land-management. Our objective was to evaluate spatial and temporal dynamics of soil-surface CO₂ effluxes in bioenergy-based corn (Zea mays L.) and reconstructed prairie systems. Systems evaluated included continuous corn (harvested for grain and 50% of the corn stover) with and without a cover crop, mixed prairies (harvested for aboveground biomass) with and without N fertilization, and corn–soybean [Glycine max (L.) Merr.] rotations harvested for grain. Soil-surface CO₂ effluxes, soil temperature, and soil water contents were monitored weekly from July 2008 to September 2011 and hourly during portions of 2010 and 2011. Annual soil-surface CO₂ effluxes were greater in prairies than row crops and are attributed to greater plant root respiration. Soil-surface CO₂ effluxes spatially varied among intra-crop management zones only for continuous corn with stover removal. However, the cover crop reduced CO₂ efflux spatial variability 70% of the time as compared to stover removal without a cover crop. Spatial variability of effluxes was not explained by soil physical properties or conditions. Temperature-induced diurnal fluctuations of CO₂ effluxes were not evident during apparent soil–water redistribution. Further research on the mechanisms behind this process is needed followed by incorporation of mechanisms into CO₂efflux models.