Apple pomace includes seeds that are rich in protein, fiber, and oil, which can be extracted from them. However, they can also contain a significant amount of toxigenic amygdalin. We hypothesized that amygdalin is a compound that significantly reduces the nutritional and health quality of defatted apple seeds. An experiment was conducted on rats that were distributed into three groups and fed with high-fructose diets. In the control (C) and amygdalin (AMG) groups, cellulose and casein were the source of dietary fiber and protein, respectively; in the apple seed meal (ASM) group, dietary fiber and protein originated from the endosperm of apple seeds, which were previously defatted and ground. A diet fed to the ASM group also contained 0.24% of amygdalin from the meal, whereas the AMG diet was supplemented with the same amount of synthetic amygdalin. After 14 days of experimental feeding, the body weight of rats was decreased in the ASM group. When compared to the C group, apparent protein digestibility and nitrogen retention were increased in the AMG group, while both were decreased in the ASM group. In the small intestine, mucosal maltase activity was decreased in the AMG and ASM groups, whereas lactase activity was only decreased by dietary amygdalin. The caecal SCFA pool and butyrate concentration were significantly increased in the ASM group compared to the other groups. Moreover, the ASM diet increased plasma concentration of high density lipoprotein (HDL) cholesterol and plasma antioxidant capacity of water-soluble substances (ACW). It also decreased the liver content of thiobarbituric acid-reactive substances (TBARS). In contrast, dietary amygdalin did not affect these indices. Dietary supplementation with apple seed meal can exert beneficial effects on the intestinal tract, blood lipid profile and antioxidant status of rats. In most cases, these effects are not limited by the presence of amygdalin. However, the nutritional value of protein from apple seed meal is relatively low.