The use of forest biomass to produce energy is increasingly viewed as a means to reduce fossil fuel consumption and mitigate global warming. However, the impact of such practices on soils in the long term is not well known. We revisited forest plots that were subjected to either whole-tree (WTH, n = 86) or stem-only (SOH, n = 110) harvesting 30 years ago in the boreal forest in Quebec, Canada. The objective of the present study was to find soil properties that could explain the lower soil C and N stocks at the sites subjected to WTH compared to SOH after 30 years. Compared to SOH, lower soil C and N stocks attributable to WTH occurred when soil particle content <20 µm was below 30%. The theoretical separation of soil organic matter into two fractions according to soil particle content <20 µm-a recalcitrant and a labile fraction-could explain the observed pattern of soil C and N differences between WTH and SOH. Imperfect or poor soil drainage conditions were also associated with lower soil C and N in WTH compared to SOH. Limiting additional biomass harvesting from these sites would help to preserve soil C and N from potential losses.