Extracellular phenoloxidase enzymes play an important role in the stability of soil carbon storage by contributing to the cycling of complex recalcitrant phenolic compounds. Climate warming could affect peatland functioning through an alteration of polyphenol/phenoloxidase interplay, which could lead them to becoming weaker sinks of carbon. Here, we assessed the seasonal variability of total phenolics and phenoloxidases subjected to 2–3 °C increase in air temperature using open-top chambers. The measurements were performed along a narrow fen–bog ecological gradient over one growing season. Climate warming had a weak effect on phenoloxidases, but reduced phenolics in both fen and bog areas. Multivariate analyses revealed a split between the areas and also showed that climate warming exacerbated the seasonal variability of polyphenols, culminating in a destabilization of the carbon cycle. A negative relationship between polyphenols and phenoloxidases was recorded in controls and climate treatments suggesting an inhibitory effect of phenolics on phenoloxidases. Any significant decrease of phenolics through repeatedly elevated temperature would greatly impact the ecosystem functioning and carbon cycle through an alteration of the interaction of polyphenols with microbial communities and the production of extracellular enzymes. Our climate treatments did not have the same impact along the fen–bog gradient and suggested that not all the peatland habitats would respond similarly to climate forcing.