Soil contamination by bisphenol A (BPA) has raised considerable ecological and environmental concerns, particularly due to its potential impact on plant growth. However, the interactive effects of BPA and different soil types on soil–plant systems remain poorly understood. Capsicum annuum L., a widely cultivated vegetable crop, was used as a model to systematically investigate the mechanisms of BPA uptake, translocation, and metabolic disruption in roots under varying soil types and BPA concentrations. Greenhouse experiments showed that BPA accumulation in pepper roots was highest in clay soil, significantly greater than in sandy or loamy soils. When BPA concentrations exceeded 10 mg/kg, root elongation and vitality were markedly suppressed, accompanied by enhanced antioxidant enzyme activity and elevated malondialdehyde content, indicating increased oxidative stress. Integrated transcriptomic and metabolomic analyses identified 995 differentially expressed genes and revealed significant disruptions in root metabolic processes. BPA stress altered the expression of genes related to the biosynthesis of hormone precursors and branched metabolites. Key pathways, including indole-3-acetic acid biosynthesis and hormone signal transduction, were significantly affected. These findings clarify the soil-dependent uptake and translocation patterns of BPA in pepper roots and provide important molecular insights into the plant’s adaptive and defense responses under BPA-induced stress.