The effect of ten commercial prebiotics on the growth ability of four Lactobacillus strains was studied to develop a synbiotic product. The prebiotic score was calculated to assess the capability of prebiotics that stimulated the growth of Lactobacillus compared to potential pathogens. Although both galacto-oligosaccharide (GOS) and lactitol (LAC) could enhance growth, LAC had a highest prebiotic score value for four Lactobacillus strains. Survival of encapsulated synbiotics forming by Lactobacillus casei 30–1 and LAC in simulated gastrointestinal condition was evaluated. 15 g l−1 LAC provided effective protection with 72.62% encapsulation efficiency and a 3.65 logs reduction. The microcapsules were then added into yoghurt and the result showed that there was an increased survival of probiotics due to the protection of cells by microencapsulation and the promoting effect of LAC on the probiotics growth. However, yoghurt with synbiotic microcapsules showed a reduced quality compared to controls over the storage period. This study had shown that microencapsulation and addition of LAC help to enhance the survival of probiotic stains in yoghurts during storage, but had a negative relationship between the improvement of yoghurt quality and the addition of synbiotic microcapsules.