Biomass harvest generates an imbalance in forest carbon (C) and nitrogen (N) cycles and the nonlinear biogeochemical responses may have long-term consequences for soil fertility and sustainable management. We analyze these dynamics and characterize the impact of biomass harvest and N fertilization on soil biogeochemistry and ecosystem yield with an ecosystem model of intermediate complexity that couples plant and soil C and N cycles. Two harvest schemes are modeled: continuous harvest at low intensity and periodic clear-cut harvest. Continuously-harvested systems sustain N harvest at steady-state under net mineralization conditions, which depends on the C:N ratio and respiration rate of decomposers. Further, linear stability analysis reveals steady-state harvest regimes are associated with stable foci, indicating oscillations in C and N pools that decay with time after harvest. Modeled ecosystems under periodic clear-cut harvest operate in a limit-cycle with net mineralization on average. However, when N limitation is strong, soil C–N cycling switches between net immobilization and net mineralization through time. The model predicts an optimal rotation length associated with a maximum sustainable yield (MSY) and minimum external N losses. Through non-linear plant–soil feedbacks triggered by harvest, strong N limitation promotes short periods of immobilization and mineral N retention, which alter the relation between MSY and N losses. Rotational systems use N more efficiently than continuous systems with equivalent biomass yield as immobilization protects mineral N from leaching losses. These results highlight dynamic soil C–N cycle responses to harvest strategy that influence a range of functional characteristics, including N retention, leaching, and biomass yield.