The purpose of this research made Cuko Pempek as functional food by supplementing BAL to produce Cuko pempek probiotic. The existence of anti-microbial and anti-bacterial Cuko pempek components became obstacles, therefore it needed strategy to answer two main issues that was first, still allowe the existence of capsaicin and alisin which was caracter impact of Cuko pempek; and second, to protect BAL in order to survive. The strategy was the encapsulation prepared according to Sheu and Marshall, (1993) and the preparation of Cuko pempek modified from ID, (2012). The result showed that the encapsulation of Cuko pempek probiotic with cold storage at temperature of 12oC produced viability with the average number of cells reaching the range of 109, 108, and 107 and the shelf life until the 20th day even some units until the 30th day. The encapsulation of Cuko pempek probiotic with storage at temperature of 27oC produced viability with the average number of cells reaching the range of 109, 108, and 107 and the shelf life until the 10th day even some units reaching the 20th day, but in the 8th day there was contamination in 5 experimental units, on the 10th day increased 5 contaminated units, and on the 12th day increased 3 units and on the 13th day occurred Sacharomyces contaminant on all experimental units.