Pigeonpea cultivation in drylands faces challenges such as unpredictable rainfall, poor crop establishment, and management issues, necessitating the development of innovative, science-based technologies, particularly in a climate change context. This study was conducted in a split-split plot design, with two sowing methods (direct sowing and transplanting), two cropping systems (sole pigeonpea and pigeonpea intercrop with soybean), and three genotypes (ICPH3762, ICPH2740, and Maruti). The results showed that transplanting pigeonpea seedlings was the most effective sowing method, with a significant yield increase of 9.5 to 17.8% over direct sowing. Despite high yield in sole pigeonpea, pigeonpea + soybean intercrop had 9.97 to 17.90% higher system equivalent yield (SEY). The ICPH2740 outperformed other genotypes, yielding 10.15 to 15.57% more than ICPH3762 and 23.56 to 45.43% more than Maruti. Transplanting also improved system water productivity by 19.90%, resulting in a higher sustainable yield index (0.64) and a higher soil organic carbon stock (10.29 Mg ha-1). Correlation and PLSR analyses confirmed strong relationships between soil organic carbon, N, P, K, Zn, B, and yields, with transplanted pigeonpea performing better than the other treatments. Bayesian models indicated a 71% probability that transplanting increases pigeonpea yield and SEY compared to direct sowing. The intercropping demonstrated enhanced overall system yields, with stable, higher yields observed with the ICPH2740. Further, the yield benefits of transplanting were not affected by dry spells. This research advocates the use of transplanted pigeonpea as a climate-adaptive, sustainable strategy to maximize productivity and resilience in similar dryland agroecosystems under a climate-changing scenario.