Twisted disease caused by Fusarium is one of the causes of the decline in shallot production in Indonesia. Disease management by adding Casuarina leaf litter and maize leaf litter during planting time has suppressed twisted disease incidence and increased shallot production in previous studies. Bacterial communities can influence disease suppression and increase plant production in soil. However, the effect of adding Casuarina and maize leaf litter on the soil bacterial community, and its impact on suppressing twisted disease is still unknown in shallot planting. In addition, no further studies have been conducted on the effectiveness of the application time of Casuarina and maize leaf litter. This study aimed to determine the best application time of leaf litter in suppressing twisted disease, the effect of changes in soil bacterial communities, and bacteria that act as core microbe, biomarkers, and keystone taxa. Results showed that adding Casuarina and maize leaf litter during planting time was more effective than adding Casuarina and maize leaf litter two weeks before planting. The diversity and abundance of bacteria in soil with the addition of Casuarina leaf litter (C) were higher than those of maize leaf litter (J). In addition, Pseudarthrobacter was found in group C, which acts as a core microbe, biomarker, and keystone taxa that may be able to suppress pathogens that cause twisted disease. Paenibacillus acts as a core microbe, biomarker, and keystone taxa in group J, which may increase shallot production. This study's results will help develop effective twisted disease management strategies to control disease development.