Purpose <p>Vidalia onions are known globally for their characteristically low pungencies and remain a vital part of the economy in Southeast Georgia, USA, where they are grown. Previous research has shown that variability in soil properties (e.g. soil type, texture, and sulfur concentration) can affect onion pungency. </p> Methods <p>The objectives of this study were to (i) examine the spatial variability in soil properties within four Vidalia onion fields during the 2020 and 2021 growing seasons, and (ii) identify relationships between soil properties and onion yield and flavor profile. Each 10-ha field was intensely sampled, collecting corresponding soil and onion samples.</p> Results <p>Onion yields ranged from 8 to 66 Mg ha^− 1, and while site-year specific relationships were identified in association with yield, these relationships were not consistent across site-years. However, pungency as determined by pyruvic acid content ranges from 0.78 to 6.98 µmol mL^− 1 and was positively associated with soil organic matter and pH in both surface and subsurface soil horizons and negatively correlated with the depth to the subsurface claypan. Meanwhile, pungency showed a mixed or nonsignificant relationship to soil sulfur in the surface soil horizons, suggesting sulfur availability is determined by the interaction of soil properties and not absolute soil sulfur content. </p> Conclusion <p>These results indicate that the physical and chemical differences among soils within individual fields were sufficient to affect nutrient availability and alter onion flavor. Overall, the results of this study point to the utilization of site-specific fertilizer recommendations and management plans to ensure consistency of onion quality in the Vidalia growing region.</p>