Developing fruit is considered as an excellent model to study the complex network of metabolites which are altered rapidly during development. Metabolomics revealed that developing psyllium fruit is a rich source of primary metabolites (ω-3 and ω-6 fatty acids and amino-acids), secondary metabolites and natural antioxidants. Eidonomy and anatomy confirmed that psyllium fruit followed five stages of development. Total lipids and fatty acids were synthesized differentially; saturated fatty acids (FAs) increased, whereas total polyunsaturated FAs decreased with increasing developmental stage. The unsaturation index and degree of unsaturation showed a catenary curve. Principal component analysis confirmed a significant shift in the FA profile from bud initiation to the maturation stage. Similarly, a similar level of total amino acids was present at different developmental stage following a temporal biosynthesis pathway. Total phenolic and flavonoid contents decreased in tandem with fruit development. Twenty-two different metabolites were identified, and metabolic changes were also observed during fruit development. Six metabolites were detected exclusively in the flowering stage, whereas two were detected in each of early and maturity stages of development. The metabolites apigenin and kaempferol were detected ubiquitously in all developmental stages. Time-dependent metabolomics revealed a shift in metabolite biosynthesis. During fruit development, metabolites, FAs, amino acids, total phenolics, total flavonoids, antioxidants and scavenging activities changed progressively and were co-ordinately linked to each other. As a future perspective, further studies will focus on the validation of identified metabolites, which integrated with transcriptomics data and will reveal the metabolic regulatory network of development psyllium fruit.