Historical logging practices and fire exclusion have reduced the proportion of pine in mixed-conifer forests of the western United States. To better understand pine’s decline, we investigate the impact of historical logging on the tree regeneration layer and subsequent stand development over almost a century of fire exclusion. We use a unique dataset derived from contemporary (∼2016) remeasurement of 440 historical quadrats (∼4m²) in the central Sierra Nevada, California, in which overstory trees, tree regeneration, and microsite conditions were measured and mapped both before and after logging in 1928–1929. We found that pine made up only 12% of the prefire regeneration layer despite comprising 32% of nearby adult basal area. Pine relative abundance changed little with logging and declined to 5% of the contemporary regeneration layer. In contrast, the relative abundance of incense-cedar regeneration (32%) already outpaced its representation in the overstory (17% by basal area) before logging and proceeded to dominate the contemporary understory (49%). We did not find strong evidence for the positive influence of gaps on pine regeneration in any time period. However, across species, post-logging skid trails were positively associated with regeneration and woody debris was negatively associated with regeneration in at least one time period. We discovered that the occurrence of advance regeneration (regeneration that preceded and survived logging) best predicted new contemporary trees across all species. For shade-tolerant species, post-logging regeneration that established up to ten years after logging was also associated with new contemporary trees. In contrast, the few pine that transitioned into the contemporary canopy during the study period all established prior to logging. Our work provides evidence that low pine abundance in the regeneration layer as early as 1928 contributed to low rates of pine in the overstory in 2016, showcasing that the decline of pine likely began before logging and official federal fire suppression policies. We suggest that fire exclusion before logging perpetuated shifts towards shade-tolerant and fire-intolerant species in the regeneration layer that were early and lasting.