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Plant endosymbionts (endophytes) influence host plant health and express genotype-dependent ecological relationships with plant hosts. A fungal species intended to confer host plant resistance to a forest pathogen was used as inoculum to test for effects of inoculation on disease resistance, microbiomes, and phytochemistry of a threatened pine species planted in a restoration setting. Correlations of inoculation presence/absence, phytochemistry, spatial location of seedlings, maternal seed sources, and fungal endophytic communities in the foliage of six-year-old whitebark pine (Pinus albicaulis) seedlings were assessed five years after an experimental inoculation of seedlings with foliar endophytic fungi cultured from whitebark pine trees at Crater Lake National Park, including Paramyrothecium roridum. We hypothesized that P. roridum would modify host microbiomes in a manner that combats white pine blister rust disease. Our assessment of seedlings in the field five years after inoculation allowed us to consider whether inoculation stimulated long-lasting changes in microbiome communities and whether effects varied by seedling genetic family. Tests for effects of endophyte inoculation on disease resistance were inconclusive due to current low levels of rust infection observed at the field site. Foliar fungal endophyte richness and Shannon diversity varied with maternal seed sources. Isotopic stoichiometry and phytochemistry did not vary with seedling spatial proximity, inoculation treatment, or maternal seed family. However, endophyte community composition varied with both seedling spatial proximity and maternal seed sources. Endophytic communities did not vary with the inoculation treatment, and the hypothesized biocontrol was not detected in inoculated seedlings. We draw three conclusions from this work: (1) fungal microbiomes of whitebark pine seedlings across our study site did not vary with host phytochemical signatures of ecophysiological status, (2) the inoculation of P. albicaulis seedlings with a mixture of fungal endophytes did not lead to persistent systemic changes in seedling foliar microbiomes, and (3) in correspondence with other studies, our data suggest that maternal seed source and spatial patterns influence fungal endophyte community composition.