Bacillus species are well known for their ability to efficiently control root nematodes in plants, particularly those causing root lesions, such as Pratylenchus spp. However, the effectiveness of this control can vary among different Bacillus species. Additionally, these bacteria can influence rhizosphere microbial communities, further contributing to nematode suppression. In this study, we evaluated the effects of B. subtilis and B. amyloliquefaciens, both individually and in co-inoculation, on the suppression of Pratylenchus spp. and on shifts in the rhizosphere microbial communities of lima bean (Phaseolus lunatus) genotypes, including landraces and improved lines. Specifically, we assessed Pratylenchus spp. populations in soil and root samples following bacterial application. Moreover, we analyzed potential changes in the rhizosphere microbial communities of these genotypes. Our results revealed that inoculation with both Bacillus species reduced Pratylenchus populations in the roots, with B. subtilis exhibiting stronger suppression effects, particularly in the lima bean landrace. Co-inoculation increased microbial richness and diversity in the rhizosphere. The rhizosphere microbiome was dominated by Actinobacteria, Proteobacteria, and Firmicutes, with B. subtilis and B. amyloliquefaciens influencing the abundance of specific bacterial genera. Inoculation also altered predicted functions related to nitrogen cycling and organic matter processing, revealing genotype-specific microbial responses. This study demonstrates that both Bacillus species can effectively suppress Pratylenchus in lima bean roots and distinctly shape rhizosphere microbial communities.