Micronutrient malnutrition is one of the most serious health challenges facing vast sectors of Africa's population, particularly resource‐poor women and children. Development and utilization of drought‐tolerant, biofortified varieties is probably the most effective, sustainable, and potentially long‐lasting strategy for reducing micronutrient deficiencies and coping with frequent droughts. Our objective was to develop second‐generation biofortified bean (Phaseolus vulgaris L.) varieties combining drought tolerance, multiple disease resistance, and higher concentrations of iron and zinc in grain than the first‐generation varieties currently grown by farmers in east, central, and west Africa. Forty‐seven F2 populations segregating for mineral density, resistance to biotic and abiotic stress factors, marketable grain types, and yield potential were developed at Kabete Field Station, and advanced to F4 as population bulks. During the 2010 long rain season, 6,612 F4 single plants were selected and used to establish F4.5 progeny rows during the 2011 short rain season at Kabete. These progenies were evaluated for resistance to angular leaf spot, anthracnose, root rots, and agronomic traits. In 2012, 102 F4.6 lines were evaluated under drought stress and no‐stress conditions at Kabete and Thika. During the 2012 short rain season, selected disease and drought‐tolerant F4.7 lines were evaluated for mineral density and for their agronomic potential at four locations representing major bean production environments. Results showed significant (p < 0.01) variation for mineral density, drought tolerance, disease resistance, growth habit, grain type, and maturity among the populations and their progenies. Iron concentration varied from 30 to 130 ppm. Zinc concentration varied from 10 to 60 ppm. Superior lines were selected from BF01, BF07, BF16, and BF36 populations. Eighty‐four lines had 50% more yield under stress and no‐stress conditions compared with the parental lines, suggesting transgressive segregation. Results indicate that varieties combining high micronutrient density, resistance to diseases and drought, and marketable grain types can be developed from these populations.