Human-induced changes in atmospheric composition are expected to affect primary productivity across terrestrial biomes. Recent changes in productivity have been observed in many forest ecosystems, but low-latitude upper tree line forests remain to be investigated. Here, we use dendrochronological methods and isotopic analysis to examine changes in productivity, and their physiological basis, in Abies religiosa (Ar) and Pinus hartwegii (Ph) trees growing in high-elevation forests of central Mexico. Six sites were selected across a longitudinal transect (Transverse Volcanic Axis), from the Pacific Ocean toward the Gulf of Mexico, where mature dominant trees were sampled at altitudes ranging from 3200 to 4000 m asl. A total of 60 Ar and 84 Ph trees were analyzed to describe changes in growth (annual-resolution) and isotopic composition (decadal-resolution) since the early 1900s. Our results show an initial widespread increase in basal area increment (BAI) during the first half of the past century. However, BAI has decreased significantly since the 1950s with accentuated decline after the 1980s in both species and across sites. We found a consistent reduction in atmosphere to wood 13C discrimination, resulting from increasing water use efficiency (20–60%), coinciding with rising atmospheric CO2. Changes in 13C discrimination were not followed, however, by shifts in tree ring δ18O, indicating site- and species-specific differences in water source or uptake strategy. Our results indicate that CO2 stimulation has not been enough to counteract warming-induced drought stress, but other stressors, such as progressive nutrient limitation, could also have contributed to growth decline. Future studies should explore the distinct role of resource limitation (water vs. nutrients) in modulating the response of high-elevation ecosystems to atmospheric change.