Stream export of nitrogen (N) as nitrate (NO3−; the most mobile form of N) from forest ecosystems is thought to be controlled largely by plant uptake of inorganic N, such that reduced demand for plant N during the non-growing season and following disturbances results in increased stream NO3− export. The roles of microbes and soils in ecosystem N retention are less clear, but are the dominant controls on N export when plant uptake is low. We used a mass balance approach to investigate soil N retention during winter (December through March) at the Hubbard Brook Experimental Forest by comparing NO3− inputs (atmospheric deposition), internal production (soil microbial nitrification), and stream output. We focused on months when plant N uptake is nearly zero and the potential for N export is high. Although winter months accounted for only 10–15% of annual net nitrification, soil NO3− production (0.8–1.0 g N m−2 winter−1) was much greater than stream export (0.03–0.19 N m−2 winter−1). Soil NO3− retention in two consecutive winters was high (96% of combined NO3− deposition and soil production; year 1) even following severe plant disturbance caused by an ice-storm (84%; year 2) We show that soil NO3− retention is surprisingly high even when N demand by plants is low. Our study highlights the need to better understand mechanisms of N retention during the non-growing season to predict how ecosystems will respond to high inputs of atmospheric N, disturbance, and climate change.