Simultaneous infections of host plants with endophytic fungi are common in both natural and agricultural ecosystems. Endophyte-infected (E+) grasses may differ in chemical composition and root exudates from endophyte-free (E-) individuals, and these differences may indirectly affect soil properties and microbial communities in the host grass habitat. In this study, we used as plant material Achnatherum sibiricum, a native grass, naturally infected with two species of endophytes, including Epichloë sibirica and E. gansuensis. E. gansuensis has two morphotypes, E. gansuensis-1 and E. gansuensis-2,of which E. gansuensis-1 exhibits strict vertical transmission, while E. gansuensis-2 can be transmitted vertically as well as horizontally. The objective of this study was to explore the effect of endophyte infection, endophyte species, nitrogen availability, and maternal plant genotype on the physicochemical properties and microbial communities of soil in the A. sibiricum habitat. At the end of a pot experiment, we analyzed the soil total carbon (C) and nitrogen (N), determined soil pH, and estimated the soil C mineralization. Soil microbial biomass and community composition were assayed by using the phospholipid fatty acid (PLFA) technique. In the present study, we found that the soil pH value differed significantly between the E+ and E- treatments (E+ > E-). In addition, the soil pH was influenced by endophyte species: pH in the E. sibirica-infected condition was higher than that in the E. gansuense-1 infected condition, but the difference was not significant with the E. gansuense-2 condition. Endophyte infection significantly improved the total amount of rhizosphere microorganisms but reduced soil bacterial:fungal ratio. Endophyte status and species, nitrogen addition, and maternal plant genotype had no significant effects on soil total carbon (C) and nitrogen (N), rhizosphere microorganisms and C mineralization ability. This study suggested that endophyte infection could alter soil pH and microbial community structure, and endophytic fungi may change soil total C and N with more available nitrogen or in the long-term. These conclusions provided some experimental basis for further understanding the complex symbiotic relationship between fungal endophytes and native grasses and its role in ecosystem C and N cycling.