Our main objective was to trace and to quantify the stabilization of nitrogen released from litter decomposition in different functional soil organic matter fractions. To identify the fate of nitrogen in a free-range experiment, 15N-labeled beech litter was deposited on the bare soil surface of three 2 m × 2 m plots on a Rendzic Leptosol under beech (Fagus sylvatica L.) with mull humus form near Tuttlingen (Swabian Jura, Germany). The 15N composition of bulk soil and soil fractions was monitored for three years by sampling the litter layer and the Ah horizon (0–5, 5–10 cm) after 140, 507, and 876 d. A combined density and particle size fractionation procedure allowed the isolation of different functional soil organic matter fractions: free light fraction, occluded organic matter, and organo-mineral associations. The first flush in the 15N enrichment was observed in the bulk soil within 140 d, due to plant debris transferred to the free light fraction by probably bioturbation and soluble compounds being leached from the litter directly to the clay fractions. The observed rates within the first 140 d indicated a quick transfer of 15N-enriched compounds from litter into the free light fraction, with a rate of 0.07 μg kg−1 d−1, and to the clay fractions, with a rate of 0.31 μg kg−1 d−1. In contrast, transfer to the occluded light fractions was delayed, with rates of 0.01 μg kg−1 d−1 (> 20 μm) and 0.001 μg kg−1 d−1 (< 20 μm), respectively. After 876 d, we recovered 9% of the added label in the 0–10 cm soil horizon, of which more than 4% was found in the organo-mineral fraction (0–5 cm), nearly 3% in the light fractions (0–5 cm), and another 2% unspecified in the bulk soil of 5–10 cm depth. We therefore conclude that the clay fractions act as the main sink for the recovered 15N. The rapid incorporation and the high preservation of 15N in the clay fractions revealed the dominant role of organo-mineral associations in the stabilization of nitrogen in the investigated soil.