Sphagnum mosses are key to northern peatland carbon sequestration. They have a range of morphological and anatomical characteristics that allow them to cope with environmental stress. Sphagnum also produces a plethora of biochemicals that may prevent stress‐induced cell‐damage. However, the linkages between Sphagnum anatomical, morphological and biochemical traits (i.e. metabolites, pigments and antioxidant enzyme activities) are poorly known, neither are their joint responses to environmental change. Here, we quantify and link an array of Sphagnum anatomical, morphological and biochemical traits in five Sphagnum‐dominated peatlands distributed along a latitudinal gradient in Europe, covering a range of regional and local environmental conditions. Sphagnum morphological and anatomical traits were intrinsically linked to Sphagnum metabolites and enzyme activities, and these relationships were driven by shared responses to local and regional environmental factors. More particularly, we found that Sphagnum traits can be grouped into four clusters related to growth, biomass, defense and water stress tolerance. We used regional and local environmental conditions data to further show that biochemicals and their specific linkages with some morphological traits describe dimensions of physiology not captured by anatomical and morphological traits alone. These results suggest that Sphagnum morphology and function is rooted in the metabolome, and that incorporating biochemicals into the functional trait space concept can enhance our mechanistic understanding and predictive power in Sphagnum ecology.