Current and future ozone concentrations have the potential to reduce plant growth and increase carbon demand for defence and repair processes, which may result in reduced carbon sink strength of forest trees in long-term. Still, there is limited understanding regarding the alterations in plant metabolism and variation in ozone tolerance among tree species and genotypes. Therefore, this paper aims to study changes in birch leaf metabolome due to long-term realistic ozone stress and to relate these shifts in the metabolism with growth responses. Two European white birch (Betula pendula Roth) genotypes showing different ozone sensitivity were growing under 1.4–1.7 × ambient ozone in open-field conditions in Central Finland. After seven growing seasons, the trees were analysed for changes in leaf metabolite profiling, based on 339 low molecular weight compounds (including phenolics, polar and lipophilic compounds, and pigments) and related whole-tree growth responses. Genotype caused most of the variance of metabolite concentrations, while ozone concentration was the second principal component explaining the metabolome profiling. The main ozone caused changes included increases in quercetin-phenolic compounds and compounds related to leaf cuticular wax layer, whereas several compounds related to carbohydrate metabolism and function of chloroplast membranes and pigments (such as chlorophyll-related phytol derivatives) were decreasing. Some candidate compounds such as surface wax-related squalene, 1-dotriacontanol, and dotriacontane, providing growth-related tolerance against ozone were demonstrated. This study indicated that current growth-based ozone risk assessment methods are inadequate, because they ignore ecophysiological impacts due to alterations in leaf chemistry.