Marginal lands are an untapped source of agricultural potential, particularly regarding high‐yielding, low‐input bioenergy crops like Miscanthus × giganteus (Miscanthus). Miscanthus is of specific interest because it can be productive and sequester carbon in soil even under the stressful conditions present on some degraded lands. A key component of these abilities is the interaction of Miscanthus with its soil and root microbiome. Microbial functions depend on the nutrient status of soil, and hence are sensitive to fertilization regimes. Nevertheless, little is known about how fertilization strategies affect the partnership of Miscanthus with its microbial associates. Here, we tested the individual and interactive effects of nutrient addition and bioaugmentation (i.e., the addition of microbial communities) on Miscanthus performance and microbiome function in marginal soil. We found that the effect of nutrient addition on Miscanthus biomass yield depended on nutrient addition type (i.e., organic or inorganic nutrients) and whether bioaugmentation was also applied. Some microbial functions, like free‐living nitrogen fixation and carbon use efficiency, were sensitive to nutrient addition depending on whether bioaugmentation was also applied. On the other hand, arbuscular mycorrhizal fungus colonization of roots decreased with fertilization regardless of bioaugmentation. These results imply that managing microbial communities may regulate the effect of nutrient addition on plant–microbe interactions that in part determine system productivity and environmental impact.