The within-farm-spatial-variation of soybean yields has been a major obstacle to maximize yields in Pennsylvania and other soybean growing states. The underlying causes behind such yield variations are currently unknown. The objective of this study was to investigate whether variation in selected biological and chemical properties of soil contribute to spatial heterogeneity of soybean yields. Fourteen locations in Pennsylvania were chosen for this study. Bulk soil samples were collected from five historically high and low yielding sites per location at V1 growth stage. The plant pathogenic nematode counts (lesion, stunt, spiral, stubby root, dagger, ring, lance, and pin), fungal counts (Fusarium, Pythium, and Phytophthora species and Rhizoctonia solani), organic matter, cation exchange capacity, pH, and nutrients (P, K, Mg, Ca, Zn, Cu, S) of soil samples were determined. Based on ANOVA, none of the measured variables was significantly different between high and low yielding sites. The principle component analysis (PCA) revealed that first two PCs contribute to 46% of the total observed variation in the data set. However, this variance maximizing data point distribution failed to distinctly cluster high and low yielding sites in the PC space. Findings suggested that the underlying biological and chemical causes behind within-farm spatial-heterogeneity of soybean yields in Pennsylvania is more complex and beyond the scope of the variables investigated in this study.