In comparison to classical fruit juice processing, polyphenols and dietary fiber can be extracted from pomace by means of pectinases and cellulases. In the present study, rats were fed with such produced extraction juices from apples, grapes, and red beets as drinking fluids instead of water for 4 weeks to evaluate their physiological effects. In all test groups, the intake of extraction juices was greater as compared to control (water intake), resulting in a higher urine excretion. In the apple and grape group, pH values in feces was lower than control. Administration of extraction juices from apples increased fecal counts of Lactobacillus and Bifidobacterium. More acetate and total short-chain fatty acids appeared in intestinal contents of the apple and red beet group. Furthermore, the intestinal contents of test groups contained higher concentrations of primary bile acids, cholesterol, and cholesterol metabolites but lower concentrations of secondary bile acids. The total amount of steroids excreted by these groups was also greater than control. Quercetin and isorhamnetin appeared in urine of rats fed extraction juices from apples and grapes; in urine of the former group, phloretin was found also. Administration of the extraction juices, enriched in secondary plant metabolites and dietary fiber, resulted in beneficial nutritional effects in rats.