Lactobacillus plantarum and Bifidobacterium lactis were co-encapsulated separately with either inulin or resistant starch in Ca-alginate/chitosan microcapsules by electro-hydrodynamic atomization (EHDA). Encapsulation yield of core materials and their release profile were studied. Protective role of polysaccharide matrix on bacteria under gastrointestinal (GI) conditions and storage at 25, 4 or −18 °C were investigated. Encapsulation yield was calculated to be 98, 79 and 99 percent for bacteria, inulin and resistant starch, respectively. Ten percent of inulin was expelled from the Ca-alginate network into water after 24 h; however, no resistant starch was released. Chitosan coating reduced the release of inulin by up to 5 percent. Survival studies showed 5.90 ± 0.3 log CFU/g of Lb. plantarum and 7.19 ± 0.15 log CFU/g of B. lactis survived GI conditions in starch-containing microcapsules. Viability loss of Lb. plantarum was successfully restricted during storage at room temperature by encapsulation in Inulin-containing microcapsules as 6.33 ± 0.21 log CFU/g survived after 90 days storage. The findings revealed EHDA can be employed for co-encapsulation of probiotics and high molecular weight prebiotics in micron-sized capsules which could open up a new perspective for targeted delivery of live cells to the colon through foods.