Understanding the processes controlling peatland carbon (C) sequestration is critical to anticipate potential changes in the global C cycle in response to climate change. Although identification of these factors may be relatively straightforward on seasonal timescales, at centennial to millennial timescales complexities arise because of interactions between climate, vegetation, hydrology and long-term ecological processes. To better understand the factors controlling long-term C accumulation, Holocene rates of C sequestration were quantified from three pristine ombrotrophic peatlands in boreal Quebec, northeastern Canada (52°N, 75–76°W). Bulk density and loss-on-ignition analyses, combined with radiocarbon dating and age–depth modelling, were used to estimate long-term apparent rates of carbon accumulation. Past changes in vegetation and water-table depth were obtained from plant macrofossil and testate amoeba analysis. Earliest regional peat accumulation started ~7520 cal. BP, with long-term rates of C sequestration varying between 14.9 and 22.6 g/m² per yr. High C sequestration rates occurred during the mid Holocene when relatively stable Sphagnum section Acutifolia communities were present, while low rates were found during the cooler late Holocene when Cyperaceae and ligneous vegetation were more dominant. However, C sequestration was highly variable among cores, implying that local topography, geomorphology and hydrology, or disturbance factors such as fire, mediate the influence of climate on C accumulation. Reconstructed water-table depths reveal several dry shifts since 3000 cal. BP, suggesting that episodic cold and dry conditions during the late Holocene may have contributed to lower C sequestration rates. Given the intensity of the water-table shifts at these times, we hypothesize that recurrent episodes of frozen subsurface peat might have intensified surface drying. As projected by climate scenarios, anticipated warmer and wetter conditions may lead to greater stability of hummock Sphagna cover and increased C sequestration potential in boreal peatlands.