In recent time, there has been an increase interest to improve prebiotic material and probiotic bacteria mainly in food. This study aims to evaluate the effect of Jerusalem artichoke (JR) and Cyprus esculents (Tigernut or Chufa) (TN) as prebiotics source, to improve growth and survival of probiotic bacteria in yoghurt and as a preserved agent against the food borne bacteria in vitro. In addition, emphasis on improve nutritional value of dough using a new source of inulin by supplemented wheat flour with JR and TN. In vitro JR and TN were used as prebiotic for evaluation their effect as growth promoters for prebiotic bacteria (Lactobacillus plantarum, Lactobacillus curvatus and Bacillus subtilis) and evaluated antimicrobial activity against Staphylococcus aureus at different concentrations (5.0 and 10.0%). The results revealed that JR and TN contained of a sufficient amount of macronutrients carbohydrate, fiber and valuable amino acids. Sugar profile of these plants showed that, inulin was the most abundant polysaccharides in JR while TN was abundant in fructose. These polysaccharides (inulin and fructose) as considered as bioactive ingredients and prebiotic compounds. In addition, 10 % supplementation level of JR or TN resulted in greater growth rates of prebiotic bacteria, as well asshowed stronger antimicrobial activity. Therefore, these results could suggest a preferential utilization of JR and TN in the people diet for improving the nutritional value and provide health benefits as functional foods, as well as considered economic and natural antimicrobial agent in food preservation.