Pigeonpea [Cajanus cajan (L.) Millspaugh] is a vital, nutrient-rich legume predominantly cultivated in arid and semi-arid regions of the world. Despite its agronomic importance, comprehensive morphophysiological variability research in pigeonpea remains limited. The present investigation aimed to assess the genetic variability across 200 pigeonpea genotypes (193 pigeonpea genotypes and 7 check cultivars) using eight yield-contributing traits alongside four physiological parameters: nitrogen balance index (NBI), chlorophyll index (CI), flavonoid content (FC), and anthocyanin content (AC). Morphological traits were characterized using standard plant descriptors for pigeonpea across the various growth stages. Significant genetic variability was detected for all 12 traits through joint analysis of variance. Correlation analysis revealed that seed yield/plant (SYPP) was positively associated with number of pods/plant (NPP), number of branches/plant (NBP), 100-seed weight (HSW), NBI, CI, plant height (PH) and number of seeds/pod (NSP). Path coefficient analysis indicated that NPP, NBI, NBP and HSW directly contributed most significantly to SYPP. Principal component analysis (PCA) identified four principal components explaining 68.32% of the total variability, while cluster analysis grouped genotypes into eight distinct clusters. The genotypes AH 16-36, AL 882, ICPL-20338, AH 09-36, AH 16-38 and AL 2019 demonstrated superior morphophysiological traits, indicating their potential for use in pigeonpea improvement programs. Notably, this study integrates non-destructive assessments of physiological traits (NBI, CI, FC, AC) with morphological characterization, offering a novel framework for dissecting genetic variability in pigeonpea. The findings underscore the potential of these genotypes for enhancing crop productivity and resilience. Hence, future research should focus on the validation of these genotypes under multi-environment trials and exploration of marker-assisted breeding for physiological traits linked to stress tolerance and yield improvement.