Fire exclusion over the last two centuries has driven a significant fire deficit in the forests of western North America, leading to widespread changes in the composition and structure of these historically fire-adapted ecosystems. Fuel treatments have been increasingly applied over the last few decades to mitigate fire hazard, yet it is unclear whether these fuel-focused treatments restore the fire-adapted conditions and species that will allow forests to persist into the future. A vital prerequisite of restoring fire-adaptedness is ongoing establishment of fire-tolerant tree species, and both the type and reoccurrence of fuel treatments are likely to strongly influence stand trajectories. Here, we leveraged a long-term study of repeated fuel treatments in a Sierra Nevada mixed-conifer forest to examine the regeneration response of six native tree species to the repeated application of common fuel treatments: prescribed fire, mechanical, mechanical plus fire, and untreated controls. Our objectives were to (1) quantify differences in forest structure and composition following the repeated application of alternative fuel treatments that may influence the establishment environment and then (2) identify the stand structure and climate conditions influencing seedling dynamics. We found that both treatment type and intensity are highly influential in shifting forests toward more fire-adapted conditions and determining species-specific regeneration dynamics. Specifically, the conifer species tracked here increased in either colonization or persistence potential following repeated applications of fire, indicating fire may be most effective for restoring regeneration conditions broadly across species. Fire alone, however, was not enough to promote fire-adapted composition, with concurrent mechanical treatments creating more favorable conditions for promoting colonization and increasing abundances of fire-tolerant ponderosa pine. Yet, even with repeated fuel treatment application, establishment of fire-intolerant species far exceeded that of fire-tolerant species over this 20-year study period. Moreover, increasing growing season water stress negatively impacted seedling dynamics across all species regardless of treatment type and intensity, an important consideration for ongoing management under heightened climatic stress. While repeated treatments are waypoints in restoring fire-adapted conditions, more intense treatments via gap-creation or hotter prescribed fires targeting removal of fire-intolerant species will be necessary to sustain recruitment of fire-tolerant species.