Prolonged summer droughts are projected to occur as a consequence of climate change in Central Europe. The resulting reduced soil water availability may lead to alterations in rates of soil processes such as nitrogen partitioning among soil organic matter fractions and stabilization within soil. To study the effect of climate change-induced drought on (1) the distribution of nitrogen among soil organic matter fractions and (2) nitrogen stabilization, we performed a space-for-time climate change experiment. We transferred intact plant–soil–microbe mesocosms of a Rendzic Leptosol with a young beech tree from a slope with northwestern exposure in southern Germany characterized by a cool-moist microclimate across a narrow valley to a slope with southwestern exposure with a warm-dry microclimate, which reflects projected future climatic conditions. A control transfer was also done on the northwest-facing slope within the same area of origin. We combined a homogenous 15N labeling approach using ammonium nitrate with a physical fractionation procedure and chemical soil extraction protocols. Our aim was to follow the partitioning of 15N in different soil organic matter fractions, i.e. light fractions, organo-mineral fractions, and extractable soil fractions including microbial biomass, ammonium, nitrate, and dissolved organic nitrogen. Within less than one growing season, we observed a modified partitioning of recently applied inorganic 15N between different soil fractions in relation to drier summer conditions, with attenuated nitrogen turnover under drought and consequently significantly higher 15N concentrations in the relatively labile light fractions. We ascribed this effect to a decelerated mineralization immobilization turnover. We conclude that prolonged summer droughts may alter the stabilization dynamics because the induced inactivity of microorganisms may reduce the transfer of nitrogen to stabilization pathways. A retarded stabilization in organo-mineral associations enhances the risk of nitrogen losses during extreme rainfall events, which are projected to increase in the 21st century predicted by future climate change scenarios for Central Europe.