Background: For a probiotic to be viable it needs to be preserved at a recommended minimum level of 6-7 log 10 cfu/g in the product being consumed, as suggested by the International Dairy Federation. Different biopolymer matrices have been used for encapsulation of probiotic; however, loss of viability is still a challenge. Materials and Methods: Modified citrus pectin-alginate microbeads containing Lactobacillus acidophilus ATCC 4356 was developed. Efficiency of the microbeads was evaluated in simulated conditions of the gastrointestinal tract and in Balb/c mice induced with colon tumor. Genomic identification of faecal lactobacilli samples from treated mice was also performed. Results: The Modified citrus pectin-alginate probiotic microbeads significantly enhanced the viability of Lactobacillus acidophilus ATCC 4356 compared to the control (p< 0.05) both in vitro and in vivo. Exposure of the modified citrus pectin-alginate microbeads to 3 hours of simulated gastric juice resulted in 82.7% survival of L. acidophilus ATCC 4356. Also, the number of faecal lactobacilli in the modified citrus pectin-alginate probiotic treated mice increased by 10.2% after 28 days. Conclusion: Modified citrus pectin-alginate is a novel effective means of oral delivery of bacterial cells and bioactive compounds. Modified citrus pectin-alginate can be used in probiotic therapy which may improve the prevention of colon cancer.