In recent decades, the rising severity of summer heatwaves has increased the co-occurrence of heat and drought stress leading to forest mortality and to reductions in crop yield. Plant responses to this combined stress can be unique from the response to either independent stress, yet few studies have investigated these responses in tree species. Our work examines adjustment of several primary metabolites and polyamine (stress indicating secondary metabolites) in paper birch and white spruce subjected to two seasons of repeated heatwaves, drought, and elevated CO₂. Our objectives were to determine if the metabolic adjustments in response to heatwave+drought stress are: 1) unique or shared with either individual stress; 2) greater in birch compared to spruce; and 3) carried over into the following season. Our data show that white spruce displayed many metabolic responses that were unique to the combined stress, especially in the first year, while paper birch displayed few. Further, the unique responses in spruce seen in the first season stress exposure did not carry into the following season indicating possible stress memory. Our data highlights the importance of considering species-specific responses to multiple stressors when making predictions about forest response to future climate scenarios.