Impacts of forest management practices on soil carbon (C) and nitrogen (N) dynamics remain under debate due to complex interactions between belowground biogeochemical processes. To optimize practices that minimize soil C and N losses, we investigated the effects of management practices on soil C and N fluxes, including the leaching of dissolved organic C (DOC) and N, by comparing clearcutting, stem girdling (removal of the bark and phloem tissue), and control treatments in a Japanese cedar plantation. Canopy opening by clearcutting is hypothesized to have a greater effect on soil C loss and the leaching of nitrate-N relative to girdling. Results showed that clearcutting increased soil heterotrophic respiration (organic matter decomposition) and lead to a loss of soil organic C (2.9–3.7 Mg C ha−1 yr−1). Higher litter inputs from girdled tree dieback caused an increase in DOC fluxes from the organic horizon, whereas the loss of fresh litter inputs decreased DOC fluxes from the organic horizon following clearcutting. Clearcutting increased nitrate-N leaching by 3.3–4.8 kg N ha−1 yr−1 due to the loss of plant N uptake and the increased mineralization of soil organic matter, but high C/N ratios in dissolved organic matter limited nitrate leaching in the girdled treatment. Effects of forest management practices on soil C loss and nitrate leaching loss could be variable, but the slash application in clearcutting and the slow dieback in stem girdling could mitigate soil C loss and nitrate leaching loss.