Anthropogenic-based disturbances may alter peatland soil–plant causal associations and their ability to sequester carbon. Likewise, it is unclear how the vegetation attributes are linked with different soil C decomposition-based pools (i.e., live moss, debris, and poorly- to highly-decomposed peat) under grassing and harvesting conditions. Therefore, we aimed to assess the relationships between aboveground vegetation attributes and belowground C pools in a Northern Patagonian peatland of Sphagnum magellanicum with disturbed and undisturbed areas. We used ordination to depict the main C pool and floristic gradients and structural equation modeling (SEM) to explore the direct and indirect relationships among these variables. In addition, we evaluated whether attributes derived from plant functional types (PFTs) are better suited to predict soil C pools than attributes derived from species gradients. We found that the floristic composition of the peatland can be classified into three categories that follow the C pool gradient. These categories correspond to (1) woody species, such as Baccharis patagonica, (2) water-logged species like Juncus procerus, and (3) grasslands. We depicted that these classes are reliable indicators of soil C decomposition stages. However, the relationships change between management. We found a clear statistical trend showing a decrease of live moss, debris, and poorly-decomposed C pools in the disturbed area. We also depicted that plant diversity, plant height, and PFT composition were reliable indicators of C decomposition only under undisturbed conditions, while the species-based attributes consistently yielded better overall results predicting soil C pools than PFT-based attributes. Our results imply that managed peatlands of Northern Patagonia with active grassing and harvesting activities, even if small-scaled, will significantly alter their future C sequestration capacities by decreasing their live and poorly-decomposed components. Finally, aboveground vegetation attributes cannot be used as proxies of soil C decomposition in disturbed peatlands as they no longer relate to decomposition stages.