In poultry, severe gastrointestinal diseases are caused by bacteria and coccidia, with important economic losses in the poultry industry and requirement of treatments which, for years, were based on the use of antibiotics and chemotherapies. Furthermore, Salmonella spp., Clostridium perfringens, and Campylobacter jejuni can cause serious foodborne diseases in people, resulting from consumption of poultry meat, eggs, and derived products. With the spread of antibiotic resistance, which affects both animals and humans, the restriction of antibiotic use in livestock production and the identification of a list of “critically important antimicrobials” became necessary. For this reason, researchers focused on natural compounds and effective alternatives to prevent gastrointestinal disease in poultry. This review summarizes the results of several studies published in the last decade, describing the use of different nutraceutical or phytonutrients in poultry industry. The results of the use of these products are not always encouraging. While some of the alternatives have proven to be very promising, further studies will be needed to verify the efficacy and practical applicability of other compounds.