The predominant cropping system in the Central Great Plains, winter Wheat-Fallow (W-F) rotation, is associated with decreases in Soil Organic Matter (SOM) primarily because of tillage during the fallow period. Intensive cropping with reduced tillage and fallow are practices that provide more residues, which may increase SOM and improve soil quality parameters. Our study evaluated selected soil properties related to soil quality in research plots established in 1990 on a Weld loam (fine, smectitic, mesic aridic Paleustolls). Various cropping intensities with several rotations were evaluated. We investigated the effects of cropping intensity on soil organic C, aggregate-size distribution, particulate organic matter, soil microbial communities, and enzymatic activities of C and N cycling. Soil samples were fractionated into two groups of aggregate size: macroaggregates (>250 μm) and microaggregates (<250 μm) by wet sieving. Relative to W-F conventional tillage, continuous cropping increased soil total C by an average of 0.3 Mg C ha^-1 yr^-1 to the depth of 15 cm. Macroaggregate was affected by tillage but not by cropping intensity. Enzyme activity of β-glucosaminidase, β-glucosidase, and α-galactosidase were affected by rotation phase and fallow frequency. Principal Component Analyses (PCA) of Fatty Acid Methyl Ester (FAME) profiles showed shifts in the microbial community structure between the alternative systems compared with W-F rotation. For this soil, fourteen years of continuous cropping and no-tillage with reduced fallow frequency have a positive effect on nutrient cycling, soil C storage, and soil biochemical functioning.