Conifer forests historically have been resilient to wildfires in part due to thick organic soil layers that regulate combustion and post-fire moisture and vegetation change. However, recent shifts in fire activity in western North America may be overwhelming these resilience mechanisms with potential impacts for energy and carbon exchange. Here, we quantify the long-term recovery of the organic soil layer and its carbon pools across 511 forested plots. Our plots span ~ 140,000 km2 across two ecozones of the Northwest Territories, Canada, and allowed us to investigate the impacts of time-after-fire, site moisture class, and dominant canopy type on soil organic layer thickness and associated carbon stocks. Despite thinner soil organic layers in xeric plots immediately after fire, these drier stands supported faster post-fire recovery of the soil organic layer than in mesic plots. Unlike xeric or mesic stands, post-fire soil carbon accumulation rates in hydric plots were negligible despite wetter forested plots having greater soil organic carbon stocks immediately post-fire compared to other stands. While permafrost and high-water tables inhibit combustion and maintain thick organic soils immediately after fire, our results suggest that these wet stands are not recovering their pre-fire carbon stocks on a century timescale. We show that canopy conversion from black spruce to jack pine or deciduous dominance could reduce organic soil carbon stocks by 60–80% depending on stand age. Our two main findings—decreasing organic soil carbon storage with increasing deciduous cover and the lack of post-fire SOL recovery in hydric sites—have implications for the turnover time of carbon stocks in the western boreal forest region and also will impact energy fluxes by controlling albedo and surface soil moisture.