Cleistocalyx nervosum var. paniala juice or makiang juice has high content of acid and phenolic compounds which are detrimental to probiotic bacteria. The screening of potential probiotic with acid production and phenolic tolerant bacteria from fermented tea leaves revealed 5 isolates which were identified using 16s rRNA sequencing procedure and found similarity to the strain of Lactobacillus plantarum in GenBank database at 98–100%. The storage of 5 isolates and 6 probiotics in makiang juice for 24 h was indicated that L. plantarum MF105 and TISTR 2074 showed the least reduction of 30.10 ± 1.25 and 61.41 ± 2.37%, respectively. These cultures were encapsulated in 2% alginate bead (Al), Al + single-layer of gelatin (ACG), and Al + double-layer of gelatin (ACGD). They were kept in makiang juice at 4 °C. The physico-chemical characteristics of beads in makiang juice illustrated that the accumulation of phenolic compounds was faster than the pH decreasing and caused initial reduction of bacterial viability. The ACGD beads absorbed slower and accumulated less amount of phenolic compounds than others. They were the most effective in cell protection, the viability of encapsulated MF105 and TISTR2074 were prolonged to more than 7 and 4 days, respectively. Cell adaptation in combination with encapsulation enhanced the survival of probiotic cell in sub-lethal stress conditions. Data had shown that increasing the coating layer provided a chance to improve lethality of probiotic bacteria.