In the age of biofuel innovation, bioenergy crop sustainability assessment has determined how candidate systems alter the carbon (C) and nitrogen (N) cycle. These research efforts revealed how perennial crops, such as switchgrass, increase belowground soil organic carbon (SOC) and lose less N than annual crops, like maize. As demand for bioenergy increases, land managers will need to choose whether to invest in food or fuel cropping systems. However, little research has focused on the C and N cycle impacts of reverting purpose-grown perennial bioenergy crops back to annual cropping systems. We investigated this knowledge gap by measuring C and N pools and fluxes over 2 years following reversion of a mature switchgrass stand to an annual maize rotation. The most striking treatment difference was in ecosystem respiration (ER), with the maize-converted treatment showing the highest respiration flux of 2,073.63 (± 367.20) g C m−2 year−1 compared to the switchgrass 1,412.70 (± 28.72) g C m−2 year−1 and maize-control treatments 1,699.16 (± 234.79) g C m−2 year−1. This difference was likely driven by increased heterotrophic respiration of belowground switchgrass necromass in the maize-converted treatment. Predictions from the DayCent model showed it would take approximately 5 years for SOC dynamics in the converted treatment to return to conditions of the maize-control treatment. N losses were highest from the maize-converted treatment when compared to undisturbed switchgrass and maize-control, particularly during the first conversion year. These results show substantial C and N losses occur within the first 2 years after reversion of switchgrass to maize. Given farmers are likely to rotate between perennial and annual crops in the future to meet market demands, our results indicate that improvements to the land conversion approach are needed to preserve SOC built up by perennial crops to maintain the long-term ecological sustainability of bioenergy cropping systems.