Organic farming is regarded as a promising agricultural management practice to maintain a sustainable ecosystem. However, organic farming often has lower yields than conventional farming, which might be due to the different quantities and qualities of nutrients applied through fertilization in these two contrasting farming practices. Given that nutrient conversion in soil is largely driven by the presence and activities of microorganisms, we investigated here how bacterial communities and biochemical processes respond to fertilizers with different C/N ratios in organically managed soil. We measured responses in the microbial C and N utilization patterns, bacterial compositions, and soil properties over a period of 56 days. This revealed a positive correlation between N assimilation into microbial biomass and the C/N ratios of fertilizers. However, this relationship was also impacted by bacteria introduced along with the fertilizer, in particular with alfalfa. Together our results demonstrate the differential responses that bacterial communities have to different types of fertilizers. This information will contribute to a better management of organic soil with the long-term aim of improving productivity.