The plant rhizosphere plays a key role in plant function and immunity. Apple Replant Disease (ARD) is a dysbiosis in the apple rhizosphere environment in locations that have a history of apple cultivation. Due to increased intensification of apple growing systems and land scarcity, ARD incidence is on the rise and can result in a 50% loss of profitability to growers. Soil fumigation is a common practice for mitigating ARD but has limited efficacy and is not allowed in some countries because of its potential for environmental damage and human harm. Using resistant rootstocks is a key strategy in overcoming ARD. To understand rootstock resistance, it is important to describe and characterize rhizosphere microbial communities of various rootstocks in an environment conducive to microbial health. We planted an organically managed apple orchard with 15 different rootstocks in a randomized complete block design. In both 2022 and 2023, we sampled the soil adhering to the roots of these trees and extracted DNA from it in order to characterize both bacterial and fungal microorganisms in the rhizosphere of the rootstocks in our research. We also established an aeroponic greenhouse trial to sample rhizodeposits from six of the rootstocks used in the orchard trial, with the aim of characterizing plant metabolites that are exuded from roots with untargeted HPLC/LCMS. Bacterial species richness was elevated in rootstocks G.935 and G.11 compared to B.10, G.210, and M.9337, but did not show significant differences in other measures of alpha diversity that incorporate evenness. Bacterial beta diversity differed in 2023, but not 2022. Fungal community diversity (both alpha and beta measures) did not differ significantly by rootstock for either year. Pseudomonas and Trichoderma relative abundance were significantly different for some rootstock genotypes. Nine plant secondary metabolites were detected that differed according to rootstock genotype. Neither study revealed clear biological indicators for ARD resistance, but the results suggest that rootstock genotype does have some influence on soil microbial diversity and community as well as tree root exudation patterns.