Switchgrass intercropped with loblolly pine plantations can provide valuable feedstock for bioenergy production while providing ancillary benefits like controlling competing vegetation and enhancing soil C. Better understanding of the impact of intercropping on pine and switchgrass productivity is required for evaluating the long-term sustainability of this agroforestry system, along with the impacts on soil C dynamics (soil CO2 efflux; RS). RS is the result of root respiration (RA) and heterotrophic respiration (RH), which are used to estimate net C ecosystem exchange. We measured RS in intercropped and monoculture stands of loblolly pine (Pinus taeda L.) and switchgrass (Panicum virgatum L.). The root exclusion core technique was used to estimate RA and RH. The results showed pure switchgrass had significantly higher RS rates (July, August and September), root biomass and length relative to intercropped switchgrass, while there were no significant changes in RS and roots between intercropped and monoculture loblolly pine stands. A significant decrease in switchgrass root productivity in the intercropped stands versus monoculture stands could account for differences in the observed RS. The proportions of RS attributed to RA in the intercropped stand were 31% and 22% in the summer and fall respectively, indicating that the majority of the RS was heterotrophic-driven. Ancillary benefits provided by planting switchgrass between unutilized pine rows can be considered unless the goal is to increase switchgrass production.