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Little is known about the fruit quality of albino mutants, due to generally exhibited lethal phenotypes caused by restrained photosynthesis and energy metabolism. In this study, a non-lethal bud mutant of jujube that could bear fruit with higher nutrient content after leaf albinism was described. Compared to normal mature fruit, the albino fruit contained lower soluble sugar and titratable acid, as well as higher ascorbic acid, phenols and flavonoids contents. Through metabolome and transcriptome analyses, 109, 117, and 126 differentially accumulated metabolites (DAMs) and 1169, 797, and 3059 differentially expressed genes (DEGs) were identified in the young, white-ripened, and mature stages of albino and normal fruits, respectively. KEGG annotation indicated that DEGs and DAMs were mainly enriched in phenylpropanoid and flavonoid biosynthesis, glutathione metabolism, and α-linolenic acid metabolism. Moreover, ADH, GST17, and POD16were identified as hub genes that play major roles in high abundance of chalcone, (−)-epigallocatechin, GSH, and total ascorbate. The alteration of bioactive substance content in albino fruits was an adaptive molecular mechanism that responded to adverse mutations, and reflected a higher antioxidant capacity. These findings provide new insights into bioactive compounds accumulation in albino mutants, and provide experimental evidence for albino fruit as a potential nutraceutical or functional food.