Disease control in smallholder pig farms has not been appropriately taken care of on Samosir Island. Pig livestockers suffer a lot of losses due to bacterial infection. Reducing the bacterial population in the pigsty is beneficial for minimizing the access of animals infected with bacteria. One way is by applying a disinfectant. This study investigated the ability of alternative biodesinfectants with four concentrations to eliminate pig-associated Escherichia coli and Salmonella by in-vitro tests. Sustainable biodesinfectans are fermented fruit extract (FFE), and fermented fruits extract plus Agave sisalana (FFE +AS). The antimicrobial activity testing method was the diffusion method with a paper disc. Fermentation of fruit waste to produce FFE is more beneficial than disposing of the waste at a landfill. In this study, the fruit waste used comes from pineapple (Ananas comosus), papaya (Carica papaya), and banana (Musa paradisiaca). FEE + AS is FEE, which refermented to the addition of Agave sisalana. FFE and FFE + AS contain enzymes, organic acids, and microbial. The results showed that FEE +AS 100%, 1: 10, and 1:20 prove to inhibit Escherichia coli and Salmonella. The highest antimicrobial activity was obtained from FEE + AS with an 11.7 mm inhibition zone diameter. Further studies on disinfecting pig sheds are justified to assess their effectiveness.