This research focused on the molecular diversity of A. carambola collected from three Brazilian biomes (Cerrado, Amazônia, and Mata Atlântica), whose results revealed significant differences in metabolite profiles among these biomes through PSI‐MS analysis. Chemometric analysis provided valuable insights into the clustering patterns and metabolic distinctions. Cerrado and Mata Atlântica biomes exhibited a 70 % similarity, indicating a notable degree of resemblance. In Cerrado, carambolaside A was notably abundant, while carambolaside M was low in Amazônia and moderate in Cerrado samples. Carambolaside B was abundant in Amazônia but relatively low in the Cerrado and Mata Atlântica. In contrast, the Amazônia biome samples appeared to be more dissimilar. In Cerrado, epicatechin, kaempferol, and procyanidin B showed lower abundance, while apigenin, quercetin, myricetin, and rutin displayed moderate levels. Mata Atlântica showed relatively higher levels of kaempferol, quercetin, and rutin. This study indicated the environmental influence on secondary metabolites production in A. carambola fruits.