Understanding the dynamics of tree establishment is critical to assess forests' composition, management practices, and current responses to global change. We carried out a field seedling transplant experiment to assess not only the direct effects of resources influencing recruitment of four tree species, but also their indirect and combined effects. Our analysis integrated first growing season demographic data together with estimates of mycorrhizal fungal colonization and resource availability (light, soil moisture, and soil nitrogen). Only by considering both the direct and indirect effects of resources we were able to account for most of the variability observed during seedling recruitment. Contrary to expectations, increasing light levels were not always beneficial for recruitment even in low light habitats, and soil moisture availability benefited seedling growth but not survival. In addition, mycorrhizal fungal colonization was not always favored by high light levels or by increasing soil moisture. Seedling survival for all species was lower in plots with higher arbuscular mycorrhizal fungi, while the association with ectomycorrhizal fungi varied from beneficial to detrimental. When integrating the direct, indirect, and interactive effects of resource availability and mycorrhizal fungal colonization on tree recruitment dynamics we found that species responded in a nonlinear fashion to increasing resource levels, and we also identified thresholds, i.e., shifts in the direction of the response, along the resource gradient. Our integrated assessment considerably outperformed a null model where only direct effects of resources were accounted for. These results illustrate how the combination of direct, indirect, and combined effects of driving variables better represents the complexity of the processes determining tree species recruitment than simple resource availability mechanisms.