Increasing crop diversity has been highly recommended because of its environmental and economic benefits. However, the impacts of crop diversity on soil properties are not well documented. Thus, the present study was conducted to assess the impacts of crop diversity on selected soil quality indicators. The cropping systems investigated here included wheat (Triticum aestivum L.) grown continuously for 5 years as mono-cropping (MC), and a 5-year cropping sequence [(wheat–cover crop (CC)–corn (Zea mays L.)–pea (Pisum sativum L.) and barley (Hordeum vulgare L.)–sunflower (Helianthus annuus L.)]. Each crop was present every year. This study was conducted in the northern Great Plains of North America, and soil quality data were collected for 2016 and 2017. Selected soil quality indicators that include: soil pH, organic carbon (SOC), cold water-extractable C (CWC) and N (CWN), hot water-extractable C (HWC) and N (HWN), microbial biomass carbon (MBC), bulk density (BD), water retention (SWR), wet soil aggregate stability (WAS), and urease and β-glucoside enzyme activity were measured after the completion of 5-year rotation cycle and the following year. Crop diversity did not affect soil pH, CWC, CWN, HWC, HWN and SWR. Cropping systems that contained CC increased SOC at shallow depths compared to the systems that did not have CC. Crop diversity increased WAS, MBC, and urease and β-glucoside enzyme activity compared with the MC. Comparison of electrical conductivity (EC) measured in this study to the baseline values at the research site prior to the establishment of treatments revealed that crop rotation decreased EC over time. Results indicate that crop diversity can improve soil quality, thus promoting sustainable agriculture.