Because of increasing demands for bioenergy, a considerable amount of land in the midwestern United States could be devoted to the cultivation of second-generation bioenergy crops, such as switchgrass and miscanthus. The foliar carbon/nitrogen ratio (C/N) in these bioenergy crops at harvest is significantly higher than the ratios in replaced crops, such as corn or soybean. We show that there is a critical soil organic matter C/N ratio, where microbial biomass can be impaired as microorganisms become dependent upon net immobilization. The simulation results show that there is a threshold effect in the amount of aboveground litter input in the soil after harvest that will reach a critical organic matter C/N ratio in the soil, triggering a reduction of the soil microbial population, with significant consequences in other microbe-related processes, such as decomposition and mineralization. These thresholds are approximately 25 and 15% of aboveground biomass for switchgrass and miscanthus, respectively. These results suggest that values above these thresholds could result in a significant reduction of decomposition and mineralization, which, in turn, would enhance the sequestration of atmospheric carbon dioxide in the topsoil and reduce inorganic nitrogen losses when compared to a corn-corn-soybean rotation.