Climate change impacts on forest trees will be particularly severe for relict species endemic to the subalpine forest, such as Pinus cembra in the Alps and Carpathians. Most current knowledge about the response of this species to climate comes from tree-ring width analysis. However, this approach cannot perform in-depth and highly time-resolved analysis on the climate influence on specific growth processes and xylem functions. We analyzed xylem anatomical traits from six sites covering most of the longitudinal range of this species. Associations between climate and cell number, lumen area and cell wall thickness were computed for the 1920–2010 period using climate records aligned to degree-day temperature sum thresholds. The anatomical chronologies were clearly distinct between the Alps and Carpathians. However, climate responses were similar for all sites, suggesting common species-specific response mechanisms. Temperature showed a positive correlation with both cell number and cell wall thickness. Cell lumen size exhibited an early positive association, followed by strong negative association with temperature and a positive one with precipitation. This highlights that the cell enlargement process was negatively related to high temperature at high elevation, where meristematic processes are rather supposed to be constrained by low temperatures. Therefore, long-term climate warming can have negative consequences on the xylem potential to transport water at all investigated sites. Moreover, in the last 30 years, we observed a slight anticipation of some responses and a decrease in climate sensitivity of some xylem parameters. Our findings provide evidence of temporally unstable but spatially consistent climate response of Pinus cembra from the Alps to the Carpathians. The low diversity in xylem phenotypic responses to climate suggests that future warming could extensively and evenly affect the species throughout its entire distribution.