To optimize management, farmers require quantitative understanding of the factors affecting variability in soybean [Glycine max (L.) Merr.] seed yield and quality. Our objectives were to characterize spatial variation in soybean seed yield, oil concentration, and protein concentration in two south-central Minnesota fields over 6 yr of a corn [Zea mays L.]-soybean rotation, and to determine the influence of fertilizer treatments, soil chemical properties, and topography on soybean yield, oil, and protein. Soil and topographical variables were observed on 0.014-ha cells, and included Bray P1, Olsen P, K, Zn, pH, organic matter, total organic C, NH4-N, NO3-N, total N, mineralizable N, elevation, slope, curvature, flow accumulation, and aspect. Soybean yields consistently exhibited spatial structure. Within fields, spatial patterns of soybean yields were highly correlated across years, and we observed consistent relationships between yield and soil variables. Overall, soybean yield related positively to soil P and Zn and negatively to pH at all site-years. Models of soybean yield in relation to soil P and Zn indicate that in high pH soils at these sites, yield is optimized when soil P and Zn levels are higher than current extension recommendations. Protein and oil concentrations exhibited inconsistent spatial structure, and the spatial pattern of protein and oil concentrations differed across years. Relationships between soybean quality and soil properties were more consistent between sites within years than across years within sites, indicating that soybean quality is influenced by soil-climate interactions that function on a regional basis.