Forest management affects soil carbon (C) storage through forest composition, microclimate and litter inputs. How two major forest management systems, continuous-cover forestry (CCF) and clear-cut-based rotation forest management (RFM), differ in their impact on soil C in boreal forests is still poorly understood, however. We compared their effects on soil organic carbon (SOC) storage and quality in boreal Scots pine (Pinus sylvestris L.) dominated forests in eastern Finland. We tested the hypotheses that (1) colder microclimates and continuous litter inputs will lead to higher SOC stocks in CCF plots than in clear-cuts and (2) the more labile litter in clear-cuts with varying ground vegetation will enhance SOC decomposition rates. We sampled uncut mature forests, clear-cuts, retention-cuts and gap-cuts, in which we analysed SOC concentrations and calculated the stocks. We measured stand characteristics such as diameter-at-breast height, basal area, dominant tree height, and understorey species coverage of the various treatments and modelled the above- and belowground litter inputs based on these parameters. We used laboratory incubation and sequential fractionation of SOC to assess its degradability under standardized conditions. To estimate the decomposition rate in the various environments we incubated cellulose bags in situ. We assessed the impact of microclimate on SOC decomposition, using data from soil-temperature and soil-moisture field measurements. We quantified the microbial biomass C pool, using chloroform fumigation extraction to gain insight on the impact of forest management practice on soil microbes. The SOC concentrations and SOC stocks did not differ significantly between the treatments, despite the presence of a warmer microclimate and lower litter inputs in the clear-cut plots. However, we found differences in the quality of the SOC. Soils in clear-cut sites showed lower proportions of labile SOC compounds than did the other treatments. As hypothesized, the decomposition rates were elevated in clear-cuts, but were equally as high within the canopy gaps on gap-cut stands. Our work highlights that forest management affects the quality, degradability, long-term accumulation and storage of SOC. We conclude that the accumulation of labile compounds in uncut forests and retention-cuts, combined with the decreased decomposition rates, indicate a higher potential for future C accumulation in the soil than in clear-cuts.