Yak-Kong is a type of black soybean that is colloquially referred to as the “medicinal bean” and it elicits several beneficial effects that are relevant to human health, including attenuating the formation of skin wrinkles. It has previously been shown that soybean extracts elicit additional bioactivity that is fermented by lactic acid bacteria. In this study of lactic acid bacteria strains that were isolated from the stools of breast-feeding infants (<100 days old), we selected Bifidobacterium animalis subsp. Lactis LDTM 8102 (LDTM 8102) as the lead strain for the fermentation of Yak-Kong. We investigated the effects of LDTM 8102-fermented Yak-Kong on solar-ultraviolet irradiation (sUV)-induced wrinkle formation. In HaCaT cells, the ethanol extract of LDTM 8102-fermented Yak-Kong (EFY) effectively reduced sUV-induced matrix metalloproteinase-1 (MMP-1) secretion. The effect of EFY was superior to that of unfermented (UFY)- and Lactis KCTC 5854 (another Bifidobacterium animalis species)-fermented Yak-Kong. Additionally, EFY reduced sUV-induced MMP-1 mRNA expression and promoter activity, as well as the transactivation of AP-1 and phosphorylation of ERK1/2 and JNK1/2. Furthermore, EFY alleviated sUV-induced MMP-1 secretion, the destruction of the epidermis, and degradation of collagen in a three-dimensional (3D) skin culture model. EFY had a higher total polyphenol content and anti-oxidative activity than UFY. Twelve metabolites were significantly (≥2-fold) increased in Yak-Kong extract after fermentation by LDTM 8102. Among them, the metabolites of major isoflavones, such as 6,7,4′-trihydroxyisoflavone (THIF), exerted the reducing effect of MMP-1, which indicated that the isoflavone metabolites contributed to the effect of EFY on MMP-1 expression as active compounds. These findings suggest that EFY is a potent natural material that can potentially prevent sUV-induced wrinkle formation.