There is an increasing demand for non-dairy probiotic carriers such as fruit and vegetable juices. Probiotic Lactobacillus sanfranciscensis is predominantly used in the bakery industry, and its efficacy in fruit juices has not been studied sufficiently. Additionally, support from the carrier matrices for maintaining probiotic viability and gastrointestinal tolerance is important in selecting suitable vehicles for probiotic delivery. Three different non-dairy carrier juices (apple, orange and tomato) were tested for their ability to maintain L. sanfranciscensis viable during four weeks of refrigerated storage (4 °C). Their potential protection of L. sanfranciscensis against in vitro gastrointestinal digestion was also evaluated. Results indicated that the probiotics viability in all three juice samples met the recommended level for probiotic food (>106–107 cfu/mL) at the end of storage. However, all three juice samples showed a comparatively lower protective effect (p <0.05) on the viability of L. sanfranciscensis when exposed to simulated gastric juice (pH = 2) at the end of 60 min and simulated intestinal juice with 0.3% (w/v) bile salt (pH = 8) at the end of 240 min exposure. In general, the three tested juices can be regarded as the potential non-dairy based carriers for L. sanfranciscensis. The future research is needed to improve the modification of the probiotic carriers in order to prolong the viability of L. sanfranciscensis during the gastrointestinal digestion.