Substituting renewable forms of energy for fossil fuels is a real challenge in developed countries and fuel wood will undoubtedly have an important role to play in forested areas. However, fuel wood harvesting may deplete nutrients in forest ecosystems and adversely affect site fertility in the long term. We compared the cost of compensatory fertilising and liming operations between whole-tree harvesting and traditional stem-only harvesting. We worked in beech (Fagus sylvatica L.) stands in eastern France and two site fertility classes (high and low). We used a growth model to calculate the nitrogen, calcium, potassium, magnesium and phosphorus contents of fine woody debris (FWD, diameter < 7 cm) and compared the benefits of selling this fine wood for energy to the cost of compensatory fertilising and liming. We showed that compensating and liming are more expensive than the profits derived from selling fine fuel wood, except when fuel wood prices rise considerably. This was mainly due to the high proportion of bark in FWD compared with other tree compartments. Indeed, bark is especially rich in nutrients such as nitrogen and phosphorus, which were the most costly nutrients to replace. Our study highlights the importance of considering the environmental costs of fuel wood production at the stand scale. Whenever fertilisation or liming is necessary, we recommend compensating at least for calcium and magnesium, two nutrients that account for a very small part of the costs. In any case, fertilisation should only be used if long-term site fertility has been compromised.