Accumulating advanced glycation end-products (AGE) changes proteins' structural and functional properties and elicits many detrimental effects. This study focuses on identifying the phytometabolites present in the bioactive fraction (BF) of Musa balbisiana seed extract by GC-MS/MS. In addition, the potential of BF in mitigating methylglyoxal-induced oxidative stress and AGE formation in HepG2 cells was investigated using western blot and RT-qPCR techniques. The identification of non-targeted phytometabolites revealed the presence of 3-hydroxybenzoic acid, vanillic acid, protocatechuic acid, 4-coumaric acid, 3,4-dihydroxyphenylglycol, and catechin. BF protected fructose-induced protein glycation by reducing crosslink aggregate formation. Furthermore, BF pretreatment alleviated methylglyoxal-induced cytotoxicity in HepG2 cells by increasing the glyoxalase system and preventing AGE formation, thereby downregulating the expression of AGE receptor (RAGE). BF modulated the oxidative stress by upregulating PGC-1α expression, a regulator of mitochondrial biogenesis through activation of SIRT1 and TFAM. These findings suggest that Musa balbisiana seed can be a functional food for managing AGE and oxidative stress.