Consecutive rainfalls, due to changes in antecedent moisture, alter soil erosion processes, necessitating the implementation of suitable soil loss control methods. Biological soil microorganism approaches have been applied to control soil loss. However, information on the involvement of microorganisms in the soil loss and rill erosion processes has yet to be supplied. In this study, the individual and combined inoculation of cyanobacteria and bacteria was investigated during five consecutive rainfalls with an interval of three days, an intensity of 50 mm/h, and a duration of 30 min. Also, additional runoff simulation of about 2.18 ± 0.32 L/min was done in mid-sized experimental plots (i.e., 6 m × 1 m × 0.5 m) induced by rill erosion. These experiments were done at the Rainfall and Soil Erosion Simulation Laboratory of the Faculty of Natural Resources, Tarbiat Modares University, Iran. Soil loss and sediment concentration were measured during five consecutive rainfalls in the study treatments and compared with the control treatment. Results showed that the highest soil loss of 30,810.70 g occurred at the control treatment in the first rainfall. In contrast, individual and combined inoculation treatments of cyanobacteria and bacteria with the secretion of polysaccharides and resulting stability of aggregates decreased soil loss significantly (p < 0.01) by 99.65%, 99.91%, and 100.00%, respectively, compared to the control treatment. In the combined treatment of cyanobacteria and bacteria, soil loss further decreased by 68.38%, 70.33%, and 7.27% for 2 through 4, respectively, events and increased by 19.96% in the fifth event, and sediment concentration also decreased by 68.88% and 59.86% for the second and third events, respectively and increased by 4.66% and 83.30% for the fourth and fifth events, respectively. The best performance was found in the combined inoculation in consecutive rainfalls (i.e., from the second to the fifth event), and the bacteria treatment and the combined treatment did not significantly differ in performance (p = 0.94). The cyanobacterial treatment had a significant effect only for the first rainfall compared to the bacteria treatment. Bacteria therapy is advised as a treatment for conserving soil and water resources in rill erosion-prone regions due to the time and cost necessary to create the biomass required.