The establishment of soybean [Glycine max (L.) Merr.] seedlings are largely affected by environmental conditions, including precipitation and soil properties; these factors often affect yield. Soil clods are the product of soil properties and weather conditions. In this current study, remote sensing imagery was used to assess seedling establishment and soil clods during the emergence stage. Our study investigated the interaction among soil clods present in a field, established seedlings, and yield. The soil clods were used as surrogate covariates of soil properties in assessing the effects on yield mediated by seedling establishment. A multilevel mediation analysis using the Bayesian approach was performed. Moreover, an on-farm experiment was conducted to test several seeding rates. The presence of soil clods negatively affected seedling establishment and subsequently reduced yields. Moreover, the optimum seeding rates varied between fields. Further investigation needs to be conducted to determine how environmental factors impact yield during the reproductive stage.