Drought stress, impacting around 66% of arable land, poses a significant threat to global food security, with estimated losses of USD 37 billions, and is expected to rise due to climate change. Pigeonpea, a key legume crop in semi-arid regions, often suffers yield losses of 40–50% under drought. This study assessed 47 genetically diverse pigeonpea genotypes under well-watered and drought-stressed conditions using morpho-physiological and high-throughput phenomic traits to enhance crop resilience. Drought stress significantly reduced most traits (2.77%–68.76%), while vapour pressure deficit and proline content increased by 1–1.5 times. Phenomics-based traits like projected shoot area, convex hull area, calliper length, and near-infrared reflectance proved effective in distinguishing drought responses. Nine genotypes—ICPX140196-B-1, ICPX140203-B-1, ICPX140213-B-3, ICPX140203-B-1-5, ICPX140203-B-2, GRG-152, ICPX140205-B-4, ICPX140217-B-1, and ICPX140188-B-3—emerged as drought-tolerant, showing stable yield (≤5% loss), efficient photosynthesis, and better water status. Photosynthetic traits were strongly correlated with yield under stress and exhibited high genetic variability (10–46%) with moderate heritability, making them reliable selection criteria. This study highlights the value of integrating phenomics with traditional traits to identify drought-tolerant pigeonpea genotypes and guide future breeding strategies efficiently.