One of the main pillars of sustainable agriculture is the use of biofertilizers in agro-ecosystems to modify and reduce the use of chemical inputs. This study was carried out to investigate the effect of growth promoting bacteria on soil chemical properties in a clover-rice cropping system using a factorial experiment with randomized complete blocks having three replications at the research site of Rice Research Institute of Iran, during 2015-17. Experimental factors for clover included four levels of inoculation with symbiotic bacteria Rhizobium trifolii and four levels of inoculation with non-symbiotic plant growth promoting bacteria. The results showed that clover cultivation led to a significant increase in the percentage of soil organic carbon (1. 79%) and nitrogen (0. 216%). The Application of non-symbiotic bacteria in clover cultivation caused a significant increase in soil phosphorus in rice cultivation. The highest amount of soil phosphorus was obtained in treatments of Pseudomonas (12. 38%) and Azotobacter+ Pseudomonas (11. 8 ppm) in rice cultivation. Also, rice cultivation significant reduced available potassium in the second year (121. 1 mg/kg) compared to the first year (128. 3 mg/kg). According to the overall results of this study, the use of growth promoting bacteria while maintaining and improving the chemical properties of the soil increased the average rice yield in the second year (3250. 3 kg/ha).