Nitrogen (N)-fixing species have a function to enrich N in soil. Mixing N-fixing shrub species into poplar stands can be assumed as a measure to increase productivity while improving soil fertility. To verify this assumption and to understand the temporal influences of N-fixing shrub species mixed into poplar plantations on soil fertility, we investigated selected soil chemical and microbial properties in pure poplar (Populus × xiaozhuanica W. Y. Hsu et Liang) and mixed poplar–seabuckthorn (Hippophae rhamnoides L.) stands at ages of five and 15 years in a semi-arid region of Northeast China. Both stands at age of five have similar values of aboveground biomass, total soil organic C concentration, total N concentration, microbial biomass C, and metabolic quotient; however, at age of 15, these values except for soil metabolic quotient are significantly greater in mixed poplar–seabuckthorn stand than in pure poplar stand. The soil metabolic quotient is lower in the former stand than in the latter stand. Our results suggest that, in semi-arid regions, mixing N-fixing shrub species into poplar plantations can improve soil fertility in a long run rather than in a short term; therefore, mixing N-fixing shrub species into poplar stands is an option to improve soil fertility and increase productivity in a long run.