Microencapsulation was evaluated as a means of preserving Lactobacillus paracasei SD1, a human-derived strain with probiotic potential, in orange and aloe vera juices. The microencapsulation parameters included alginate concentration, calcium chloride concentration and hardening-time, and the efficacy of microencapsulation to preserve the survival of microencapsulated bacteria compared to free cells during exposure in fruit juices were determined. The results revealed that the viable count of free-cell form markedly decreased compared to microencapsulated form. The microencapsulation of 2% alginate (w/v) and 0.05 M CaCl2 gave the best result to preserve the probiotic. It was found that viability of microencapsulated probiotic bacteria was significantly higher than free-cell in fruit juices during 8 weeks of storage time in the refrigerator. The potential probiotic trait related to inhibitory effect was not affected after microencapsulation process. In summary, the microencapsulation method may be an alternative way of preserving the viability of probiotic L. paracasei SD1.