The target site of action of probiotics is the intestine. They must be surviving the stomach acidic condition before reaching the target site. Three probiotic bacteria were microencapsulated in sodium alginate beads using a sophisticated microencapsulation technology provided by BuCHI B-390. This study reports the tolerance of the different microencapsulated Lactobacillus at low pH using simulated gastric juice, comparing it with the tolerance of free bacteria. The three microencapsulated strains displayed time-dependent acid sensitivity at pH values under 3.0. At pH 2.0, a dramatic reduction in bacterial survival occurred after 5 min, with only L. casei surviving after 30 min, with 75% survival. At pH 2.5 microencapsulated L. casei survived for 90, L. reuteri survived for 60 and L. bulgaricus survived for only 30 min, respectively. The microencapsulation technology used in this study may effectively protect Lactobacillus from gastric conditions and permit comparisons between strains.