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Perennial crops, like switchgrass (Panicum virgatum L.), are important for bioenergy production and long-term carbon sequestration. Biochar, a byproduct of certain bioenergy production processes, is also identified as a potential tool for carbon sequestration and soil quality improvements, especially in marginal soils. Despite the focus on switchgrass, soil health characteristics under switchgrass production for biomass are unclear. This study focused on identifying the effects of four N rates (0, 17, 34, and 67 kg N ha−1) and biochar application (0 and 9 Mg ha−1) in a 3-year switchgrass field study on a silt loam soil. Soil active carbon (AC) and wet aggregate stability (WAS) were the indicators used to assess soil health. Our results indicated a decline in both AC and WAS over the study period, similar to other studies. Wet aggregate stability declined from 32% in 2018 to 15% in 2019. There were some significant differences between treatments, but no defined trends were observed. A decline in AC from 301 mg C kg soil−1 to 267 mg C kg soil−1 was also observed over the three-year period. Nitrogen rate also affected AC in the last year of study. Several possible explanations for the observed changes are proposed; however, a definitive mechanism is still unknown, thus future research is essential to improve our understanding and provide wider acceptance.