The development of biofortified and stress tolerant common bean lines contribute to counteract micronutrient malnutrition in the current condition of climate variability. Our objective was to evaluate the adaptive responses of biofortified common bean (Phaseolus vulgaris L.) lines under acidic soils and high temperature stress conditions in the Amazon region of Colombia. Adaptive responses were evaluated based on phenological, physiological and agronomic differences under combined stress conditions. A total of 247 common bean lines from the Mesoamerican gene pool were evaluated under field conditions at Florencia, Caquetá, Colombia. The common bean lines evaluated included 146 from F4 families with high iron (Fe) content and 99 common bean lines from F5 families that were obtained from simple crosses, double crosses and backcrosses among different bean lines. Lines with tolerance to combined stress conditions of acidic soil and high temperature were found with grain yields greater than 1,400 kg ha-1 from the F5 (lines: 859, 805, 865, 657) and F4 (lines: 2853, 2796) families. This improved agronomic response is likely due to the greater partitioning of photosynthates from canopy biomass (CB) toward pod formation (pod partitioning index, PPI) and grain filling (pod harvest index, PHI; harvest index, HI), which translated into higher grain yields (GY). GY was correlated with CB (r = 0.36), PPI (r = 0.6), PHI (r = 0.68), and HI (r = 0.8, P<0.001). The physiological responses that contributed toward superior agronomic performance of biofortified common bean lines include greater allocation of energy to the photosynthetic machinery (ΦII) and its dissipation in the form of heat (ΦNPQ) as the leaf temperature differential (LTD) increased under combined stress conditions. Six biofortified common bean lines (F5 lines: 859, 805, 865, 657; F4 lines: 2853, 2796) were identified with multiple stress resistance traits and these lines can serve as parents for further genetic improvement of common bean for multiple stress tolerance in the Amazon region of Colombia.