Our study addresses the first two weeks of the weaning period of piglets during which stressful physiological and environmental conditions experienced by the animals can promote the proliferation of pathogens in the digestive tract. The aim of the study was to identify new feeding strategies that result in boosting the gastrointestinal tract (GIT) microbiota of piglets and improve growth performance, reducing the negative impact of weaning. In order to identify a new synbiotic combination, 12 new putative probiotic strains of Bifidobacterium spp. and three non-digestible oligosaccharides [NDO] were screened in newly weaned piglets. The ability to increase the level of autochthonous bifidobacteria and improve growth performance were assessed. Bifidobacteria strains with a similar ability to develop in the hindgut showed a different effect on piglet performance depending on the dose in which they were provided. Our data support the idea that the presence of fructo-oligosaccharides would stimulate the occurrence of bifidobacteria in the caecum. It was shown that dietary intake of nitrate can generate salivary nitrite, which in turn is acidified in the stomach and could have antimicrobial activity against swallowed pathogens. The efficacy of the resulting synbiotic formula was improved by adding nitrate as antimicrobial. To enhance probiotic survival during gastric transit, a novel technology of microencapsulation was developed and applied to bacteria. The final synbiotic, containing the strain RA 18 of Bifidobacterium animalis subsp. lactis [1011cfu/day], the prebiotic Actilight® [4% of the diet], and nitrate [150mg KNO3/kg feed/day] was tested in organic weaned piglets reared under field conditions. Results show that the strain Ra 18 had a probiotic effect in organic weaned piglets, as it colonized and remained detectable in faecal samples until two weeks after addition. The use of our synbiotic formula improved weight gain, feed efficiency and health status of the weaned piglets.