Nutraceuticals have gained great insights in recent years due to their therapeutic implications. Secondary metabolites like glutamate, flavonoids, polyphenols and terpenoids are widespread in nature and are part of human diet. Polysaccharides of prebiotic nature are used both as therapeutic and prophylactic agents. These nutraceuticals in recent times have been reported to posses great potential to reduce antigenic and oxidative pressure in the human gut. Antioxidant rich diet is a potential therapeutic agent against reactive oxygen species induced pathogenesis. Epegenetic compounds present in antioxidant and prebiotics rich nutraceuticals mitigate and remove the causative factors associated with pathogenesis. Flavonoids and polyphenols exhibit antioxidant properties and have been recognized as potential gastroprotective agents and epigenetic modulators as well. Triterpenoids such as cucurbitacin is reported to posses anticancer activities. Glutamate is an enteric neurotransmitter that is used in improving neonatal gut function. This review comprehensively summarizes the current knowledge of gut modulating nutraceuticals which ultimately can play its role from prophylaxis of gut to its therapeutics by employing various macro and micro molecular pathways.