Biodiversity and the number of bacteria present in the soil are two of the main parameters of soil quality, especially for agricultural purposes. Analysis of the low-fertilized soils suggested that the number and diversity of the bacterial communities in this soil are low. Hence, various methods have been used to stimulate bacterial activity and improve agricultural soil conditions. One of the popular methods is the inoculation of bacteria such as <i>B. subtilis</i> and <i>R. erythropolis</i>. These bacteria are potential species as bio-inoculants in soil management. However, the effectiveness of these bacteria in stimulating the activity of bacterial communities and improving soil properties of the low-fertilized soil is still sparsely explored. Therefore, this study aimed to analyze the impact of the inoculation of <i>B. subtilis</i> and <i>R. erythropolis</i> on the bacterial community structure and soil properties of low-fertilized soil. The soil used is agricultural soil for tobacco farming activities using agrochemicals. Bacterial community structures were analyzed using the environmental DNA (eDNA) method. The soil properties analyzed were total nitrogen, carbon, phosphorous, potassium, and pH. This study suggests that <i>B. subtilis</i> and <i>R. erythropolis</i> may affect the bacterial community structure and increase the number of bacteria to reach the ideal limit for fertile soil. Adding bacterial inoculants could stimulate the growth of bacteria and the nutrient cycle in the soil environment, resulting in improved soil fertility.