Southwestern North America faces an imminent transition to a warmer, more arid climate, and it is critical to understand how these changes will affect the carbon balance of southwest ecosystems. In order to test our hypothesis that differential responses of production and respiration to temperature and moisture shape the carbon balance across a range of spatio-temporal scales, we quantified net ecosystem exchange (NEE) of CO2 and carbon storage across the New Mexico Elevational Gradient, which consists of six eddy-covariance sites representing biomes ranging from desert to subalpine conifer forest. Within sites, hotter and drier conditions were associated with an increasing advantage of respiration relative to production such that daily carbon uptake peaked at intermediate temperatures – with carbon release often occurring on the hottest days – and increased with soil moisture. Across sites, biotic adaptations modified but did not override the dominant effects of climate. Carbon uptake increased with decreasing temperature and increasing precipitation across the elevational gradient; NEE ranged from a source of ∼30 g C m−2 yr−1 in the desert grassland to a sink of ∼350 g C m−2 yr−1 in the subalpine conifer forest. Total aboveground carbon storage increased dramatically with elevation, ranging from 186 g C m−2 in the desert grassland to 26 600 g C m−2 in the subalpine conifer forest. These results make sense in the context of global patterns in NEE and biomass storage, and support that increasing temperature and decreasing moisture shift the carbon balance of ecosystems in favor of respiration, such that the potential for ecosystems to sequester and store carbon is reduced under hot and/or dry conditions. This implies that projected climate change will trigger a substantial net release of carbon in these New Mexico ecosystems (∼3 Gt CO2 statewide by the end of the century), thereby acting as a positive feedback to climate change.