Biochar applications may help ensure that stover harvest for bioenergy production is sustainable. Objectives of this study were to evaluate the effect of crop residue removal, biochar application, and traffic intensity on soil physical and chemical properties. Lump hardwood biochar produced by slow pyrolysis at ~450^oC was hammer milled to pass a 12 mm screen, surface applied, and incorporated to 10 cm on 0.11 ha field plots in Boone County, Iowa.  Continuous maize (Zea Mays) was grown for three years as part of a 22 treatment, randomized complete block study on bioenergy feedstock production. Soil quality indicators were evaluated in summer 2010 three years after the one-time biochar application of 9.8 and 18.4 Mg ha^-1 and after two stover harvests (0, ~50 and ~90% of above ground residue). Biochar significantly (P<0.05) increased average soil organic C levels from 2.40 to 2.84%, C:N ratios from 11.6 to 14.3, and pH from 5.07 to 5.32, but did not have a significant effect on total N or cation exchange capacity (CEC). Average penetration resistance was 84% greater for high-traffic compared to low-traffic interrows. Low and high biochar applications reduced penetration resistance by 6 and 8%, respectively, relative to no-biochar controls. Soil bulk density (BD) was 11% higher in high-traffic compared to low-traffic interrows.  Low and high biochar applications significantly reduced BD by 3 and 4%, respectively, for low-traffic interrows only. Residue removal significantly reduced penetration resistance and pH, but not BD, total C, total N, or CEC. The 50 and 90% harvest rates significantly reduced wet aggregate mean weight diameter by 9 and 13%, respectively, but neither biochar nor traffic intensity had a significant effect. In general, 18.4 Mg ha^-1 biochar applications resulted in small but significant improvements in several soil quality indicators despite two years of residue harvest.