The study aim was to investigate the vacuum impregnation (VI) technique for apple enrichment with quercetin glycosides from apple peel. Beside the determination of the quercetin content, structural effects on the apple parenchyma were analyzed by computerized microtomography (μCT). VI was an efficient method to enrich apples with quercetin derivatives which was affected by the apple cultivar, the vacuum pressure, the soluble solid concentration (SSC) and the viscosity of VI solution. After VI of 13 apple cultivars the quercetin content varied between 368 and 604μg/g dry mass and correlated with the firmness of the native apple and the increased apple weight. The use of low SSC solution resulted in increased quercetin enrichment in contrast to apple pectin solutions with elevated viscosity. The μCT analyses demonstrate that VI was more effective in the inner apple sections than in the outer parts. The study indicates that differences of pore size and microstructure within the apple cortex substantially affected the enrichment process.