The probiotics were susceptible to damage in commercial starters due to improper environmental conditions. In this study, the encapsulation technique was applied to improve probiotics survival using alginate, inulin (commercial and beneng taro-source), skim milk and their combination; which is prepared by the extrusion method. The survival of encapsulated probiotics in adverse environmental conditions was investigated by exposing them to low pH and heat stress. The encapsulation yield and diameter of the encapsulated probiotics were also measured before their application to yoghurt powder. Both heat stress and pH 2 resulted in the decrease of the number of viable free cells and viable encapsulated cells by about 5 log cycles and 3 log cycles, respectively. The encapsulation yield was >98% in all treatments and the diameter of probiotics was increased significantly around >2.5 mm by the encapsulation method. The viability of the encapsulated probiotic cell was decreased 1 log cycle after applying in powdered yoghurt while without encapsulation the cell count was much lower. Thus, the microencapsulation method has proven as an effective protection technique against adverse environments, especially if applied as a powder product.