Plant carbon (C) allocation is a key process determining C cycling in terrestrial ecosystems. In carbon-rich peatland ecosystems, impacts of climate change can exert a strong influence on C allocation strategies of the dominant plant species, with potentially large implications for the peatland C budget. However, little is known about plant C allocation into various secondary biosynthetic metabolites and whether different plant species vary in C allocation strategies in response to climate change. Here, we report species-specific leaf chemistry and secondary metabolism in trees (Picea mariana and Larix laricina), shrubs (Rhododendron groenlandicum and Chamaedaphne calyculata), and Sphagnum mosses (Sphagnum angustifolium and Sphagnum magellanicum) in response to whole-ecosystem warming (+0, +2.25, +4.5, +6.75 and +9 °C) and elevated CO2 manipulation (ambient or +500 ppm) in an ombrotrophic peatland. We show that warming and elevated CO2 substantially altered leaf chemistry and cuticle composition, including increases in leaf nitrogen, shifts in lipid composition and dependence on new photosynthates, although results varied by species. Shrub species lowered the saturation of their membrane fatty acids and increased their leaf nitrogen and C concentrations, while tree species increased their wax concentrations under higher warming treatments. Using isotopic labeling to trace the fate of newly-assimilated C, we observed an unexpectedly low fraction of new C in tree and shrub species (∼50% and ∼70% respectively). This suggests the combined use of newly-assimilated and older C reserves stored in plant organs for plant functional processes and CO2 originating from peat degradation and even more so in response to warmer temperatures and elevated CO2 concentrations. Under higher temperatures, Sphagnum mosses increased their leaf nitrogen but decreased their leaf C concentrations and the fraction of experiment-derived C (by 20%); suggesting an increasing C allocation to osmotic compounds that aid in maintaining high water retention capacity, albeit at the cost of other metabolites. Our results indicate species-specific shifts in plant chemistry and cuticular lipid composition, which could strongly moderate and shape boreal peatland ecosystem response to climate change in the future.