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Premise Microbial symbionts can buffer plant hosts from environmental change. Therefore, understanding how global change factors alter the associations between hosts and their microbial symbionts may improve predictions of future changes in host population dynamics and microbial diversity. Here, we investigated how one global change factor, precipitation, affected the maintenance or loss of symbiotic fungal endophytes in a C-3 grass host. Specifically, we examined the distinct responses of Epichloe (vertically transmitted and systemic) and non-epichloid endophytes (typically horizontally transmitted and localized) by considering (1) how precipitation altered associations with Epichloe and non-epichloid endophytic taxa across host ontogeny, and (2) interactive effects of water availability and Epichloe on early seedling life history stages. Methods We manipulated the presence of Epichloe amarillans in American beachgrass (Ammophila breviligulata) in a multiyear field experiment that imposed three precipitation regimes (ambient or +/- 30% rainfall). In laboratory assays, we investigated the interactive effects of water availability and Epichloe on seed viability and germination. Results Reduced precipitation decreased the incidence of Epichloe in leaves in the final sampling period, but had no effect on associations with non-epichloid taxa. Epichloe reduced the incidence of non-epichloid endophytes, including systemic p-endophytes, in seeds. Laboratory assays suggested that association with Epichloe is likely maintained, in part, due to increased seed viability and germination regardless of water availability. Conclusions Our study empirically demonstrates several pathways for plant symbionts to be lost or maintained across host ontogeny and suggests that reductions in precipitation can drive the loss of a plant's microbial symbionts.