Variations in sweetness and bitterness among Madhuca longifolia flowers strongly influence their processing value and market acceptance, yet the chemo-diversity underlying these traits remains poorly characterized. This study aimed to unravel accession- and stage-specific differences by integrating physico-biochemical, elemental, and metabolic profiling across thirteen accessions (BM-1 to BM-13) from BUAT, Banda. Sensory and textural evaluations revealed wide diversity, with BM-5 displaying superior sweetness and aroma, whereas BM-6, BM-7, and BM-10 were differentiated by firmness, elasticity, and gumminess. Biochemical analyses across flower development showed BM-5 consistently maintained higher sugars and β-carotene, while BM-1 exhibited marked reductions in sugars and total phenolics content; antioxidant activity increased with maturity, with BM-5 remaining the most stable. ICP-MS elemental analysis confirmed BM-5 as mineral-rich compared with lower-performing accessions. GC–MS metabolomic profiling of contrasting accessions (BM-1 and BM-5) across stages identified 376 volatile and semi-volatile metabolites, and multivariate analyses (PCA, VIP, volcano plots, pathway enrichment) revealed distinct stage- and accession-dependent patterns. Mature BM-5 was enriched in fermentation- and aroma-related metabolites such as melibiose, furfural, 5-HMF, and furaneol, whereas BM-1 accumulated defense-linked compounds including catechol, benzyl nitrile, and maltol. Overall, the integrated chemo-diversity landscape identifies BM-5 as a superior accession with high processing potential and value-addition prospects.