Pyrogenic organic matter (PyOM) is a product of incomplete combustion during wildfires and an important pool of soil organic carbon (SOC). The dynamics of PyOM and SOC in boreal and permafrost-affected soils are largely unknown, while storing large amounts of global carbon and being vulnerable to climate change. Here, we traced the vertical mobility, allocation in soil fractions and decomposition losses of highly 13C-labeled PyOM and its precursor ryegrass organic matter (grass OM) after two years of in-situ incubation in soil cores installed in the upper 10 cm of continuous (northern sites) and discontinuous to sporadic (southern sites) permafrost-affected forest soils in Northern Canada. At the northern sites, up to three times more PyOM was lost by decomposition (39% of initial) compared to the southern sites (11% of initial). Losses of grass OM were substantial (69–84% of initial) and larger in southern soils. The vertical incorporation was limited and >90% of recovered PyOM and grass OM were found at the applied depth (0–3 cm). The PyOM strongly interacted with mineral surfaces, as indicated by around 40% recovered in the mineral-associated heavy density fractions (<63 μm). Microscale analyses by SEM and NanoSIMS showed that PyOM was mainly allocated towards the fine fraction in a particulate and aggregated form, highlighting the importance of abiotic processes for the incorporation of PyOM in permafrost-affected soils. The grass OM was mainly recovered in the mineral fractions at southern soils with enhanced allocation towards mineral surfaces as well as increased distribution at the microscale after initial decomposition, while it remained as particulate OM in northern soils. Our results highlight that permafrost-affected boreal forest soils are sensitive to fresh PyOM and OM inputs with substantial losses. Especially PyOM persistence depended on site and soil specific properties and not solely on its physico-chemical persistence. The responses are decoupled for PyOM and non-pyrolyzed OM and require a better understanding to evaluate carbon feedbacks of high-latitude soils with global warming and associated shifts in vegetation and wildfire regimes.