Isoflavone aglycone-rich soymilk fermented by Lactobacillus delbrueckii subsp. delbrueckii, strain TUA-4408L (F4408) has stronger lipid metabolism-modulating effects than isoflavone aglycone-poor soymilk fermented by Lactobacillus delbrueckii subsp. delbrueckii, strain TUA-4404L (F4404). As such, fermentation products other than isoflavone aglycones may also exert lipid metabolism-modulating effects. Therefore, the present study aimed to compare the metabolites in soymilk (SM), F4404, and F4408 via a metabolomics approach. Various aglycones including isoflavones, flavones, flavonols, and flavanones increased in both F4404 and F4408 compared with SM. The increases in isoflavone and flavanone aglycones were greater in F4408 than in F4404. Some types of dipeptides and free amino acids, especially ornithine, increased in both fermented soymilks. The increase in free amino acids, especially ornithine, was higher in F4408 than in F4404. Thus, F4408 exhibited stronger glycosidase and protease activities than F4404. Functional components produced by lactic acid fermentation are known to improve lipid metabolism. Therefore, it is suggested that not only isoflavone aglycones but also other functional components exert lipid metabolism-modulating effects in fermented soymilks, especially soymilk fermented using TUA-4408L.