Biogas slurry is a nutrient-rich secondary product of livestock feces digestion which is recycled as a crop plantation fertilizer and provides exogenous microbes to the soil. However, the effects of biogas slurry microbes on the soil resident community remain unknown. In this study, we examined the ecological consequences of long-term biogas slurry pulse on the soil resident community and found that it promoted crop yield and altered soil characteristics. The soil microbial ecosystem was altered as a result of organic amendments due to the exogenous input of microbes and nutrients. Nevertheless, the soil resident communities were highly resilient to long-term organic pulses, as evidenced by community diversity and composition. The two dominant bacterial species in biogas slurry were Sterolibacterium and Clostridium. Notably, the abundance of Clostridium in biogas slurry increased following long-term amendments, while other species such as GP1 and Subdivision3_genera_incertae_sedis decreased; which was consistent with the results of module-eigengene analysis. Long-term organic pulses shifted the balance of microbial community assembly from stochastic to deterministic processes. Overall, our findings indicated that organic pulses accompanied with bacterial invasion could be alleviated by the resilience of soil microbial communities, thereby emphasizing the importance of microbiota assemblage and network architecture. Display omitted •Biogas slurry increased rice yields, but also induced microbial disturbance.•Soil resident communities exhibit resilience rather than resistance to long-term biogas slurry pulse.•Long-term organic pulses facilitated deterministic processes in the resident community.•Clostridium, a biomarker species in biogas slurry, increased with the amendment time.