Soils are heterogeneous at a spatial scale because of variability in soil nutrients and physical factors. The present study was conducted to investigate the heterogeneity of soil physicochemical properties in differently managed fields to determine the key factors influencing the grain yield and β-glucan content of naked waxy barley. Two fields were compared—one upland field converted from a paddy (converted upland) and one conventional upland field (normal upland). In each field, the relationships between variables were examined using correlation analyses. The results showed that the converted upland had lower yield and β-glucan content than that of the normal upland. Soil water content was a significant factor in both fields, but greater effect was observed in the converted upland. The β-glucan content was negatively correlated with soil water content in the converted upland. Electrical conductivity or mineral N was positively correlated, whereas soil penetration resistance at the depth of 20 cm-30 cm was negatively correlated with the β-glucan content in the normal upland. Comprehensive analyses indicated that avoiding water damage is the priority for increasing the yield and grain β-glucan content of naked waxy barley.