Many Bacillus species are among the plant growth-promoting rhizobacteria (PGPR) that promote the growth of many different plant species. This study aimed to investigate the effects of Bacillus thuringiensis KNU-07 on the growth of pepper plants and the soil microbiota. We also designed primers specific for the strain KNU-07 to monitor the population in pepper-cultivated soil. Accordingly, a strain-specific primer pair was designed using a database constructed from 16,160 complete bacterial genomes. We employed quantitative PCR (qPCR) to track the abundance of the strain KNU-07 introduced into pepper-cultivated soil using the strain-specific primers. Our study revealed that the strain was found to possess plant growth-promoting (PGP) activities, and it promoted the growth of pepper plants. The soil bacterial community structure due to the application of the PGPR strain was significantly changed after six weeks post-inoculation. In addition, based on qPCR analysis, the population of the introduced strain declined over time. In this study, application of a PGPR strain increased the growth of pepper plants and changed the soil bacterial community structure. The successful results of monitoring of a bacterial strain’s population using a single strain-specific primer pair can provide important information about the quantification of bio-inoculants under non-sterile soil conditions.