The effect of intensified biomass extraction on forest ecosystems is a timely question since harvest residues are increasingly utilised to produce energy and the impacts of the changed management practises are not always well understood. We compared two different modelling approaches, the MOTTI-YASSO and the EFIMOD-ROMUL model combinations, with respect to the simulated impacts of the biomass extraction in final felling on subsequent biomass and soil carbon stocks. Simulations following the latest silvicultural recommendations over a rotation were made for six Finnish forest sites varying in fertility, tree species and latitude. Model-projected effect of the intensified biomass extraction was larger with EFIMOD-ROMUL than with MOTTI-YASSO. The soil model ROMUL projected slower decomposition of organic matter than YASSO at all studied sites, which made the effect of biomass extraction on soil larger with EFIMOD. The process-based model EFIMOD-ROMUL includes feedback from soil nutrient status to productivity. With EFIMOD-ROMUL, the intensified biomass extraction decreased slightly the simulated growth of the forests and thereby the biomass carbon stock and litter input to the soil. With the empirical MOTTI model, the intensity of the simulated biomass extraction did not affect forest growth. Our results underline the importance of the selection of the modelling approach when projecting the potential effects of forest management practises on forest carbon balance.