This study is part of a larger collaborative effort to determine the overall environmental sustainability of intercropping pine (Pinus taeda L.) and switchgrass (Panicum virgatum L.), both of which are promising feedstock for bioenergy production in the Lower Coastal Plain in North Carolina. We measured soil CO₂ efflux (RS) every six weeks from January 2012 to March 2013 in four-year-old monoculture and intercropped stands of loblolly pine and switchgrass. RS is primarily the result of root respiration (RA) and microbial decomposition of organic matter (RH) releasing CO₂ as a by-product and is an important and large part of the global carbon (C) cycle. Accurate estimates of the two components of total soil respiration (RS) are required as they are functionally different processes and vary greatly spatially and temporally with species composition, temperature, moisture, productivity, and management activities. We quantified RA and RH components of RS by using a root exclusion core technique based on root carbohydrate depletion, which eliminates RA within the cores over time. We determined the relationship between RS, RA and RH measurements and roots collected from the cores. We took fresh soil cores in July 2012 to compare root productivity of loblolly pine and switchgrass in monoculture versus the co-culture. Additionally, CH₄ and N₂O fluxes were monitored quarterly using vented static chambers. Pure switchgrass had significantly higher RS rates (July, August, September), root biomass and root length in the top 0-35 cm relative to switchgrass in the co-culture, while loblolly pine with and without switchgrass had no significant changes in RS and roots. Correlations between RA and roots showed significantly positive correlation of RA to grass root biomass (r = 0.37, p ≤ 0.001), fine (r = 0.26, p ≤ 0.05) and medium root surface area (r = 0.20, p ≤ 0.1). The estimated portions of RS attributed to RA in the intercrop stand were 31% and 22% in the summer and fall, respectively. No significant treatment differences were observed in either CH₄ or N₂O flux. Our study indicates a decrease in switchgrass root productivity in the intercropped stand versus the monoculture stand which could account for differences in the observed RS.