The loss of pristine forest landscapes due to intensive management has altered forest carbon dynamics and caused a decline in biodiversity. The carbon balance of unmanaged forests is insufficiently known due to a lack of repeated measurements. Moreover, the links between the conservation of threatened species and forest carbon dynamics are poorly explored. We examined the carbon balance of boreal unmanaged forests based on three repeated tree surveys conducted in 27 unmanaged Finnish coniferous-dominated forest stands in 1990–2019. We also surveyed nationally red-listed epiphytic lichens and explored the linkages between carbon dynamics, forest naturalness, and epiphytic lichen occurrence. On average, net primary production increased by 10.7% during the study period. Still, the volume of living trees remained stable because a large proportion of the biomass growth was allocated to deadwood following tree mortality. The net primary production had a trade-off with the volume of deadwood, but in most stands, mortality was low, maintaining the trees as weak sinks. Red-listed lichen occurrence was not affected by the size of the tree carbon stock, but it was lower in stands acting as larger carbon sinks. In addition, red-listed lichen occurrence increased with estimates of stand age. Our results suggest that the studied forests maintain large carbon stocks while supporting species of conservation concern. However, more research is needed on the stability of carbon stocks in the face of shifting disturbance dynamics due to climate change. Keywords: Unmanaged forest · Carbon stock · Deadwood · Net primary production · Species richness · Epiphytic lichens.