Due to the globalization and increasing human activities, there is a significant increase in bacterial invasions to the soil ecosystems. Soil resident communities are vulnerable to bacterial invasion and suffered legacy effects after unsuccessful invasion. However, whether such changes in the soil ecosystems are permanent or temporary remains unclear. Here, we investigated the functional resilience of soil ecosystems to bacterial invasion and intensive managements. We used Escherichia coli O157:H7 (E. coli) as model strain examined the soil microbial metabolic functions, including enzyme activities, nitrogen and carbon use efficiency, community niche, and carbon metabolic potential, as well as soil physicochemical properties and microbial invader survival in 8 soil samples, 4 from natural hardwood forests and 4 from intensively managed Moso bamboo forests. The results showed that soil ecosystems were not resistant to E. coli invasion regardless of the intensity of management, which the finding was significantly reflected in the nutrient-acquiring activities or carbon utilization, or both. Besides, the invasion legacy effect (the effect after invader apoptosis) was positively related to E. coli survival time. However, most of the metabolic functions could recover almost to the initial state after 135 days of incubation, suggesting a strong recovery capacity of the soil ecosystems. These data indicate that E. coli invasion has a legacy effect on the functions of soil resident communities. However, soil ecosystems are highly resilient even under intensive human management.