High-altitude sub-Arctic ecozones are highly sensitive to climate warming, leading to shrub proliferation, canopy densification, and potentially altering carbon exchange. While temperature and moisture remain primary controls on carbon fluxes, the influence of canopy composition and phenology on surface-atmosphere carbon interactions across sub-Arctic alpine ecozones remains poorly understood. Using 25 years of CO₂ flux data pooled between three eddy covariance towers, together with plant allometry and soil carbon measurements, we characterized three elevation-defined ecological zones in the Wolf Creek Research Basin, Yukon: a lower-elevation subalpine fir forest with a sparse shrub understory near treeline (1242 masl), a mid-elevation tall, dense dwarf birch–willow shrub canopy (1314 masl), and a higher-elevation sparse dwarf birch–willow shrub tundra with interspersed lichen and moss (1421 masl). Across the study period, all sites were persistent carbon sinks. Mean annual net ecosystem productivity (NEP) was lowest at the high-elevation shrub tundra site (74 ± 37 g C m⁻² yr⁻¹), intermediate at the low-elevation forest site (100 ± 25 g C m⁻² yr⁻¹), and highest at the mid-elevation shrub site (260 ± 47 g C m⁻² yr⁻¹). Our multi-site, multi-year results indicate distinct site-specific controls on net ecosystem productivity, with differences among sites evident in magnitude, seasonal timing, and interannual variability, highlighting the role of canopy composition and phenology in shaping carbon storage and exchange. Together, these findings suggest that climate induced changes in canopy structure and phenology can alter carbon exchange across alpine ecosystems.