About 15 million hectares of peat soils have been drained for forestry in temperate and boreal zones. Increasing interest in wood biomass as a source of bioenergy has led to more intensive harvests also in peatland forests. These harvestings remove branches, needles, and stump/root systems that would earlier have remained on-site. However, in drained peatland forests, some key growth-limiting nutrients, such as potassium (K) and boron (B), are largely stored in the living tree biomass, while the stores in peat in tree rooting layer are small. A concern has thus been raised that bioenergy harvesting may induce nutrient insufficiency and decrease second rotation forest productivity. We studied the effect of whole-tree and stump harvesting on site nitrogen (N), phosphorus (P), K, and B capitals in final harvesting of a well-productive, Norway spruce-dominated peatland forest. Harvesting of stumps and above-ground harvest residues resulted in minor depletion of site N and P stores, but significant depletion of K and B. Maximizing harvest residue biomass recovery, but minimizing nutrient depletion, our results indicated that stump harvesting is a more feasible option than harvesting of above-ground residues. If above-ground harvest residues are to be harvested for bioenergy, K and B depletion may be decreased by letting the branches dry out somewhat and the needles fall down before branch harvesting. Combining our results with data on waterborne K losses suggested that K depletion may become a serious problem in second rotation forests on drained peatlands, even if harvest residues and stumps were left completely non-harvested.