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.