Giant sequoia (Sequoiadendron giganteum) is an iconic conifer that lives in relic populations on the western slopes of the California Sierra Nevada. In these settings, it is unusual among the dominant trees in that it associates with arbuscular mycorrhizal fungi rather than ectomycorrhizal fungi. However, it is unclear whether differences in microbial associations extends more broadly to non-mycorrhizal components of the soil microbial community. To address this question, we characterized microbiomes associated with giant sequoia and co-occurring sugar pine (Pinus lambertiana) by sequencing 16S and ITS1 of the bulk soil community at two groves with distinct soil parent materials. We found tree-associated differences were apparent despite a strong grove effect. Bacterial/archaeal richness was greater beneath giant sequoia than sugar pine, with a unique core community that was double the size. The tree species also harbored compositionally distinct fungal communities. This pattern depended on grove but was associated with a consistently elevated relative abundance of Hygrocybe species beneath giant sequoia. We conclude that the effects of giant sequoia extend beyond mycorrhizal mutualists to include the broader community, and that some but not all host tree differences are grove-dependent.