A long-term study was initiated in 2008 to determine effects of bioenergy sorghum [Sorghum bicolor (L.) Moench.] production on soil quality. Sorghum biomass removal may potentially deteriorate soil quality and productivity through nutrient removal and decreased organic matter return. Study treatments included continuous bioenergy sorghum and a sorghum/corn (Zea mays L.) biannual rotation, 0, 25, or 50% return of harvested sorghum biomass, no or non-limiting N addition, and a complete nutrient return treatment. The study was conducted near College Station, TX on Weswood silty clay loam soil. Soil quality indicators including soil organic carbon (SOC), total soil nitrogen (TSN), and soil C:N ratio were determined in soil samples collected annually at five depth increments to 90 cm for seven years (2009–2015) and compared to initial values in 2008. The greatest sorghum biomass yield increase from residue return was observed with 25% return and N fertilization. Nitrogen was essential for biomass and biomass C yield for both sorghum cropping systems, especially continuous sorghum. Increasing residue return from 25 to 50% tended to increase SOC in the near surface regardless of N addition, but generally not with depth. From the initial year in 2008 to 2015, SOC increased at all soil depths, except 15–30 cm, under continuous sorghum receiving residue return and N fertilization. Increases in SOC were much higher with continuous than rotated sorghum. For example, SOC storage for fertilized rotated sorghum averaged across residue return rates increased by 10% (59.4 to 65.1 Mg ha−1) and for continuous sorghum by 51% (59.4 to 90.1 Mg ha−1) by 2015 compared to initial values in 2008. For both continuous and rotated sorghum, changes in SOC stocks were greater in lower depths, principally at 30–60 and 60–90 cm, implying that SOC increases at these depths were most likely associated with bioenergy sorghum roots. After seven years of 25% residue return, SOC increased by 1.75, 5.25, 15.4, 32.9, and 39.2 Mg ha−1, respectively, at 0–5, 0–15, 0–30, 0–60, and 0–90 cm. Total soil N to 90 cm depth tended to follow similar patterns as those observed for SOC storage. Soil C:N ratio also tended to increase in all depth increments with residue return, but especially in the surface 0–5 cm with N fertilization. The highest C:N ratio increase were observed in surface soil under continuous sorghum at 25 and 50% residue return rates with or without N fertilization. Increased soil C:N at deeper depths in continuous sorghum was probably associated with sorghum roots. The return of 25% of aboveground biomass from a continuous sorghum cropping system in conjunction with N fertilization appeared feasible for maintaining soil quality in the long term.