Although global warming has the potential to increase soil CO2 efflux, the magnitude of these changes are uncertain, as CO2 production rates in deep soil are poorly constrained. In particular, management effects on the warming responses at depth are unknown. Here, we conducted an in-situ soil warming experiment down to 2.0-m depth in an agricultural Cambisol to study the warming responses of (1) CO2 production across different depths and (2) CO2 efflux from topsoil in different seasons under two management practices. To this end, we measured whole-soil profile water content, CO2 production and CO2 efflux under continuous grassland and cropland in response to elevated temperature (+4°C). Warming decreased soil water content for both management practices. We found contrasting warming effects on surface CO2 efflux, depending on season and land management practices. Subsoil CO2 production was more sensitive to warming than topsoil CO2 production with grassland subsoil showing a greater warming response than cropland subsoil. Topsoil CO2 production decreased in response to warming in the cropland but not the grassland. We concluded that warming responses of CO2 production and efflux are affected by soil management practices. Their effect on biological processes (roots and microbial activity) and factors affecting gas diffusivity, such as soil water availability and soil physical organization need to be assessed to model warming effects on carbon exchange between soil and the atmosphere in agricultural systems.