The interactions between starch and bioactive compounds (mainly polyphenols) are a topic of growing interest due to the formed complex not being digested in the small intestine of humans and a substrate by the colonic microbiota. The complex starch-polyphenol is not digested and reduces the glycemic response, this is important to control some diseases such as diabetes and metabolic syndrome. The products of colonic fermentation (short-chain fatty acids and polyphenols) have beneficial effects on human health. The bioactive compounds are complexed with the linear chains of starch, they can be partially released during digestion in the small intestine and provide antioxidant characteristics that are associated with the prevention of some diseases. Also, the polyphenols can reduce the starch hydrolysis due to the inhibition of amylases and can reduce the glycemic response due to the inhibition of glucose transporters. This chapter revised the interactions between starch and bioactive compounds, the methods to evaluate the formed complex, its effect on starch hydrolysis rate, and the bioaccessibility of the bioactive compounds after digestion in the small intestine. This information is useful in the development of functional foods with health benefits.