Interest in measuring soil quality continues to increase worldwide in view of demands on land productivity and the necessity to preserve soil resources, yet identification of suitable indicators for soil quality assessment is still evolving. This study adapted 10 biological, physical, and chemical indicators of soil quality identified by the Cornell Soil Health Test and applied them to evaluate agricultural soils in the south Willamette Valley, Oregon, USA. Soil samples from 102 sites were tested for individual indicators of soil quality that were interpreted with scoring curves developed by the CSHT. Overall soil quality scores and individual soil quality indicators were analyzed in relation to agricultural practices including cropping cycle (perennial, annual, or fallow), soil disturbance (tilled, not tilled), or management type (organic, transitional, conventional). Data analysis by forward model selection using Bayesian Information Criteria indicated that certain management practices influence soil nitrate, surface and subsurface compaction, active carbon, potentially mineralizable nitrogen, and water stable aggregation. Several soil quality indicators under organic management were found to have more favorable values than under conventional management. Soil disturbance (tillage) resulted in decreased aggregate stability compared to undisturbed soils, but was associated with increased values for certain biological indicators such as organic matter decomposition and nutrient cycling. Root colonization potential by arbuscular mycorrhizal (AM) fungi was investigated as an additional indicator of biological soil quality, and to explore underlying relationships with soil quality measures and agricultural management practices. A subset of 33 soils was tested for root colonization potential in a greenhouse bioassay with sorghum as a trap plant. Cropping cycle had a large impact on AM root colonization potential; soil samples from fields planted to perennials resulted in greater root colonization than did soils from annual fields. No other management practice significantly affected AM root colonization potential. AM root colonization potential was not related to overall soil quality scores although a weak negative relationship was observed between AM root colonization potential and two individual indicators of soil quality: soil pH and subsurface compaction. Possible reasons for the apparent lack of sensitivity by AM fungal colonization to soil quality parameters are discussed.