Current nitrogen (N) deposition rates are considerably higher than during pre-industrial times and the growing interest in forest fertilisation requires better understanding of how the N and carbon (C) cycles interact. This study is based on experimental data showing how Scots pine (Pinus sylvestris L.) forests respond to single or consecutive pulse doses of N. The data were used to support the implementation of a dynamic feedback mechanism in the Q model, allowing for changes in soil N availability to regulate the rate of decomposer efficiency. Simulations of the long-term effects of slowly increasing N deposition with and without dynamic decomposer efficiency were then compared. Both versions of the model accurately predicted the response of tree growth to N fertilisation. Slowly increasing inputs of N over a century in the modified version acted on the inputs and outputs of soil C in opposing ways: (a) rate of litter input slowed down because more N was retained in the soil and thus not available for tree growth; (b) rate of C output, through soil heterotrophic respiration, was also gradually reduced due to increasing decomposer efficiency, although not enough to sufficiently balance the reduced litter input. Accurate prediction of the amount of added N retained in the ecosystem seems to be one of the key issues for estimating enhanced C sequestration.