Changes in understory plant composition and biodiversity declines in northeastern North American forests are widespread. Preserving species and ecosystem function requires appropriate identification and management of important stressors. Coexistence of stressors, among them earthworm invasions and white‐tailed deer, makes correct identification of mechanisms that cause diversity declines challenging. We used an established factorial experiment to assess survival and growth of native seedlings (Actaea pachypoda, Aquilegia canadensis, Cornus racemosa, Quercus rubra, and Prenanthes alba) in response to presence/absence of deer and earthworms. We expected deer and earthworms to reduce seedling survival and biomass, and we evaluated potential pathways to explain this impact (soil N and P concentrations and pools, root architecture, and arbuscular mycorrhizal fungi [AMF] colonization). We developed structural equation models (SEM) to identify specific pathways through which earthworms and deer were impacting plant species with different life histories. Seedling survival was not affected by our treatments nor the plant and soil variables we tested. Actaea biomass was smaller in earthworm‐invaded plots, and with larger total N pools. In contrast, both deer and earthworm treatments were associated with lower soil nutrient concentrations, and earthworm‐invaded plots had smaller N and extractable P pools. Actaea, Cornus, Prenanthes, and Quercus seedlings had a lower proportion of fine roots in earthworm‐invaded plots, while fine roots in Aquilegia made up a higher proportion of the root system. AMF colonization in Quercus was reduced in sites colonized by earthworms, but AMF in other species were unaffected. Our SEMs showed high correlation among soil variables, but because we do not know which variables are drivers of this change and which are passengers, we can only conclude that they are changing together as deer and earthworms exert their respective influence. Different plant species responded in idiosyncratic ways to earthworm and deer effects on soil fertility, root architecture and limited effects on AMF colonization. While earthworm and deer‐mediated changes to fine roots, soil nutrients, and AMF may lead to changes in plant performance over time, these changes rarely translated to lower plant performance in our seedlings.