AbstractClimate warming and altered disturbance regimes are changing forest composition and structure worldwide. Given that species often exhibit individualistic responses to change, making predictions about the cumulative effects of multiple stressors across environmental gradients is challenging, especially in diverse communities. For example, warming temperatures are predicted to drive species upslope, whereas fire exclusion promotes the expansion of species at lower elevations where fire was historically frequent. We resampled 148 vegetation plots to assess 46 years (1969–2015) of species and community‐level response to warming and fire exclusion in a topographically complex landscape in the Klamath Mountains, California, USA, a diverse region that served as a climate refugia throughout the Holocene. We compared cover and assessed change in the elevational distributions of 12 conifer species at different life stages (i.e., seedlings, saplings, canopy). We observed consistent but non‐significant shifts upward in elevation for eight species, and a significant shift upward for one species, all of which were far less than expectations based on recent warming. Six species declined in total cover and another five declined in at least one life stage, whereas the drought‐ and fire‐intolerant Abies concolor increased by 30.7%. The largest declines were at lower elevations in drought‐tolerant, early‐seral species (Pinus lambertiana and Pinus ponderosa) and at higher elevations for the shade‐tolerant Abies magnifica var. shastensis and the regionally rare Abies lasiocarpa. Regionally rare (Picea engelmannii) and endemic (Picea breweriana) species had reductions in early life stages, portending future declines. Multivariate analyses revealed a high degree of inertia with a minor, but significant, shift in composition and a slight decrease in species turnover along the elevation gradient driven by the expansion of A. concolor. Our results indicate that most species are declining, especially at lower and mid‐elevations where fire exclusion has increased the cover of shade‐tolerant species and reduced the recruitment for fire‐adapted species. Collectively, declines in most species, insufficient upward movement to track warming, reductions in drought‐ and fire‐tolerant early‐seral species, and an increase in a single, shade‐tolerant species will leave these communities maladapted to projected climate scenarios and questions the potential for future climate refugia in this region.