We used ecosystem model simulations to study the timber and energy biomass potential offered by intensively managed cloned Norway spruce stands. More specifically, we analysed how the use of cloned trees compared with non-cloned trees, together with thinning, nitrogen (N) fertilisation and rotation length (from 60 to 100 years), affects the annual mean production of timber (i.e., saw logs, pulpwood) and energy biomass (i.e., stumps and harvesting residuals in the final felling) and its economic profitability [annual mean of net present value (NPV) with a 2% interest rate]. Furthermore, we employed a life cycle analysis/emission calculation tool to assess the total net CO2 emissions per unit of energy (kg CO2 MW h−1) produced based on energy biomass. We found that both the annual mean production of timber and the NPV increased substantially, regardless of the management regime, if cloned trees with an annual growth increase of up to 30% compared with non-cloned trees were used in regeneration. In general, the use of a short rotation with N fertilisation clearly increased the annual mean of the NPV. Consequently, the use of cloned trees also clearly increased the annual mean production of energy biomass and decreased the total net CO2 emissions per unit of energy produced based on energy biomass. However, the total annual net CO2 emissions were the lowest if a long rotation was used with N fertilisation. To conclude, the use of cloned trees together with intensive management could potentially be highly beneficial for the cost-efficient and sustainable production of timber and energy biomass in an integrated way.