Background <p>Carbon metabolism in plants involves biochemical processes such as photosynthesis, respiration, and carbon partitioning. This study aimed to elucidate the physiological and biochemical dynamics during the early development of pea seedlings (<i>Pisum sativum</i>) across five time points (6, 9, 12, 15, and 18 days) and five cultivars (Dacheong, Daehyeop 1ho, Sanghyeop, Sacheol, and Cheongmi) using semi-targeted metabolic profiling. Furthermore, we investigated the interplay between photosynthetic activity and secondary metabolite accumulation by profiling the metabolic responses of Dacheong seedlings exposed to varying photosynthetic photon flux densities (PPFDs). </p> Results <p>A total of 83 metabolites were identified. Multivariate analysis revealed similar biochemical dynamics among the five cultivars during the early seedling stage. Metabolic shifts occurred in three distinct phases: (1) an early nitrogen-rich storage metabolism phase characterized by the accumulation of asparagine and raffinose, (2) an intermediate phase marked by the accumulation of branched-chain amino acids, flavonoids, and carotenoids, and (3) a late phase characterized by increased monosaccharides and chlorophylls. These findings suggest that seedling growth relies on the mobilization and conversion of carbohydrates stored in seeds prior to the development of photosynthetic organs. Notably, significant correlations were observed between the photosynthetic pigments and secondary metabolites. Among the cultivars, Dacheong (12 days) exhibited the highest total flavonoid content (33.40 ± 1.29 mg/g). The metabolic changes in Dacheong seedlings under varying PPFD conditions indicated that higher light intensity enhanced sucrose synthesis and chloroplast component composition. Additionally, carotenoid and flavonoid levels peaking at PPFD 400 µmol/m²·s suggested that this light intensity is the optimal condition for maximizing secondary metabolite accumulation through enhanced photosynthetic activity.</p> Conclusions <p>This study is the first to profile the transition from heterotrophic to autotrophic growth in pea seedlings and reveal significant correlations between photosynthetic pigments and secondary metabolites during the seedling period. These findings provide insights into metabolic reprogramming in pea seedlings and inform strategies for enhancing their growth and nutritional quality. Future studies should include hormone analyses to further understand the metabolic transition processes in seedlings. </p> Graphical Abstract <p></p>