Forests provide valuable ecosystem and societal services, including the sequestration of carbon (C) from the atmosphere. Management practices can impact both soil C and nitrogen (N) cycling. This study examines soil organic C (SOC) and N responses to thinning and fertilization treatments. Soil was sampled at an intensively managed Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) plantation in north-western Oregon, USA. Management regimes—thinning, fertilization plus thinning, and no (control) treatment—were randomly assigned to nine 0.2-ha plots established in 1989 in a juvenile stand. Prior to harvest, forest floor and soil bulk density and chemical analysis samples were collected by depth to 150 cm. During a single rotation of ~40 years, thinning treatments significantly reduced SOC and N stocks by 25% and 27%, respectively, compared to no treatment. Most of this loss occurred in deeper soil layers (below ~20 cm). Fertilization plus thinning treatments also reduced SOC and N stocks, but not significantly. Across all management regimes, deeper soil layers comprised the majority of SOC and N stocks. This study shows that: (1) accurately quantifying and comparing SOC and N stocks requires sampling deep soil; and (2) forest management can substantially impact both surface and deep SOC and N stocks on decadal timescales.