Intercropping biofuel feedstocks in managed forests of the southeastern United States is a potentially sustainable source of renewable energy. Ecological effects of energy crops in forests are poorly understood, and it is unknown whether the ecological role of native rodents is influenced by alternative food resources. Therefore, we used a stable isotope analysis to compare diet and trophic responses of white-footed mice (Peromyscus leucopus) in 1) plots where switchgrass (Panicum virgatum), a C-4 plant, was intercropped with loblolly pine (Pinus taeda), a C-3 plant, 2) plots of loblolly pine, and 3) plots of monocropped switchgrass. We collected fur from live-trapped rodents and potential dietary sources in 2010. We predicted delta C-13 and delta N-15 values of mice in switchgrass plots would reflect a C-4-based, granivorous, diet if there was an effect of intercropping on the functional role of mice. Del(13)C values of mouse fur in monocropped switchgrass, but not intercropped switchgrass plots, shifted more toward a C-4 signal. However, delta N-15 values indicated that mice remained functionally omnivorous across treatments. Our results were supported by isotope values from invertebrates across guilds. Diet and trophic position of white-footed mice was not influenced by intercropping switchgrass in pine plantations indicating they maintained their functional role in this biofuels management regime. Future research should focus on individual and population responses of rodents to altered vegetation structure where biofuels feedstocks are grown and indirect effects on inter- and intra-species interactions. (C) 2013 Elsevier Ltd. All rights reserved.