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Green coffee is one of health-promoting supplements of the diet, applied in the form of either preparations or enriched food products. Its positive impact is manifested by mitigation of the development of certain tumors, e.g., in the colon and liver, and type 2 diabetes. Many studies proved that chlorogenic acids are the main active substances in green coffee. The bioavailability of these compounds depends among others on their interactions with other components of the diet, mainly proteins. When they are used as food ingredients, their bioavailability is additionally decreased because of the decomposition or interactions with other ingredients during food processing. The undesirable changes may be limited among others by microencapsulation, for example with β-cyclodextrin. In this study, rats were fed the pro-oxidative high fat diet, which was supplemented with chlorogenic acids from green coffee that were used in four forms such as: a purified extract, complexes of chlorogenic acids and β-cyclodextrin, and bread supplemented with either the extract or the β-cyclodextrin inclusion complex. Chlorogenic acids added to bread because of the reduced absorption from the crumb in the small intestine and increased passage to the colon, contributed to the beneficial modification of enzymatic activities of intestinal microbiota. When added directly to the diet, they contributed to the improved antioxidant status in the liver and kidneys, lowered glucose level and increased HDL level. A high ratio of reduced to oxidized glutathione in the liver and a high concentration of antioxidants in the blood serum were observed after administration of chlorogenic acids in the form of inclusion complexes with β-cyclodextrin, indicating that microencapsulation increased their bioaccessibility due to the limited interactions with other components of the diet.