Plant-based feedstocks have long been considered viable, potential sources for biofuels. However, concerns regarding production effects may outweigh gains like carbon savings. Additional information is needed to understand environmental effects of growing feedstocks, including effects on wildlife communities and populations. We used a randomized and replicated experimental design to examine initial effects of biofuel feedstock treatment options, including removal of woody biomass after clearcutting and intercropping switchgrass (Panicum virgatum), on rodents to 2 years post-treatment in regenerating pine plantations in North Carolina, USA. Rodent community composition did not change with switchgrass production or residual biomass removal treatments. Further, residual biomass removal had no influence on rodent population abundances. However,Peromyscus leucopuswas found in the greatest abundance and had the greatest survival in treatments without switchgrass. In contrast, abundance of invasiveMus musculuswas greatest in switchgrass treatments. Other native species, such asSigmodon hispidus, were not influenced by the presence of switchgrass. Our results suggest that planting of switchgrass, but not biomass removal, had species-specific effects on rodents at least 2 years post-planting in an intensively managed southern pine system. Determining ecological mechanisms underlying our observed species associations with switchgrass will be integral for understanding long-term sustainability of biofuels production in southern pine forest.