Aim: To test the effect of microencapsulation on the survival of two probiotic strains isolated from Dadih, Indonesian fermented buffalo milk, in a dynamic, computer-controlled invitro model of the upper gastrointestinal (GI) tract (TIM-1), simulating human adults. Methods and Results: Free or microencapsulated probiotics, Lactobacillus plantarum IS-10506 or Enterococcus faecium IS-27526, resuspended in milk were studied for survival in the complete TIM-1 system (stomach + small intestine) or in the gastric compartment of TIM-1 only. Hourly samples collected after the ileal-caecal valve or after the pylorus were plated on MRS agar (for Lactobacillus) or S&B agar (for Enterococcus). Survival of the free cells after transit through the complete TIM-1 system was on average for the E. faecium and L. plantarum 15.0 and 18.5% respectively. Survival of the microencapsulated E. faecium and L. plantarum was 15.7 and 84.5% respectively. The free cells were further assessed in only the gastric compartment of TIM-1. E. faecium and L. plantarum showed an average survival of 39 and 32%, respectively, after gastric passage. Conclusion: There is similar sensitivity to gastric acid as well as survival after complete upper GI tract transit of free cells, but microencapsulation only protected L. plantarum. Significance and Impact of Study: Survival of microencapsulated L. plantarum IS-10506 is increased compared to free cells in a validated invitro model of the upper GI tract. It increases its use as an ingredient of functional foods.