Soybean contributes to sustainable food and feed production, but some modern varieties favor yield at the cost of disease resistance. Using a bottom-up approach, we demonstrate that the RR2b transcription factor activates cytokinin signaling for plant growth and reproductive fitness but represses disease-resistance and root-nodulation pathways. RR2b was artificially selected during domestication and improvement, and its expression level correlate with ATT repeat polymorphisms in its promoter. Most wild soybeans and landraces have either more or less ATT repeats: more repeats lead to weak RR2b expression with lower yield and enhanced resistance to soybean bacterial blight, and fewer repeats cause strong RR2b expression, higher yield, but reduced blight resistance. Elite cultivars instead balance yield and defense via moderate RR2b expression and several ATT repeats. This confers contrasting RR2b functionality across haplotypes in response to contrasting selection pressures and offers insights into decoupling trade-offs between yield and blight resistance to enhance crop productivity.