Boreal peatlands are facing significant changes in response to a warming climate. Sphagnum mosses are key species in these ecosystems and contribute substantially to carbon sequestration. Understanding the factors driving vegetation changes on longer time scales is therefore of high importance, yet challenging since species changes are typically affected by a range of internal and external processes acting simultaneously within the system. This study presents a high‐resolution macrofossil analysis of a peat core from Store Mosse bog (south‐central Sweden), dating back to nearly 10 000 cal. a BP. The aim is to identify factors driving species changes on multidecadal to millennial timescales considering internal autogenic, internal biotic and external allogenic processes. A set of independent proxy data was used as a comparison framework to estimate changes in the bog and regional effective humidity, nutrient input and cold periods. We found that Store Mosse largely follows the expected successional pathway for a boreal peatland (i.e. lake → fen → bog). However, the system has also been affected by other interlinked factors. Of interest, we note that external nutrient input (originating from dust deposition and climate processes) has had a negative effect on Sphagnum while favouring vascular plants, and increased fire activity (driven by allogenic and autogenic factors) typically caused post‐fire, floristic wet shifts. These effects interactively caused a floristic reversal and near disappearance of a once‐established Sphagnum community, during which climate acted as an indirect driver. Overall, this study highlights that the factors driving vegetation change within the peatland are multiple and complex. Consideration of the role of interlinked factors on Sphagnum is crucial for an improved understanding of the drivers of species change on short‐ and long‐term scales.