Drought, exacerbated by climate change, is a challenge in agricultural production, especially in connection with nutrient-rich legumes like common beans, essential for sustainable food security. Selecting drought-adapted genotypes across various agricultural managements is a viable strategy to mitigate the impact of drought. This study aimed to evaluate different common bean genotypes, locally adapted and commercial ones, under different environmental factors, management practices, and water regimes to understand how the various growth conditions impact their performance and seed biochemical composition. We conducted a pioneering three-year field experiment with twelve genotypes grown under irrigated and rainfed conditions within conventional and organic farming systems. Physiological responses, seed yield, and quality parameters were evaluated and correlated to identify possible biomarkers that can be used for identifying resilient genotypes. The research found that drought and farming practices significantly affect bean yield and quality, with extreme temperatures being a key factor. Organic farming was as productive as conventional under irrigation and improved seed quality in rainfed conditions. The landrace Arrocina de Álava stood out for its tolerance and high-quality seeds under rainfed conditions, underlining the importance of locally adapted genotypes for climate resilience. The study confirmed the seed carbon isotope discrimination (Δ13C) as a reliable marker for selecting stress-tolerant genotypes and highlighted the impact of extreme temperatures on seed fat and energy content. It underscores the need for climate-adapted agriculture, highlighting organic farming as a sustainable method and the importance of incorporating climate resilience in crop breeding and management.