The fate of immobilized N in soils is one of the great uncertainties in predicting C sequestration at increased CO2 and N deposition. In a dual isotope tracer experiment (13C, 15N) within a 4-year CO2 enrichment (+200 ppmv) study with forest model ecosystems, we (i) quantified the effects of elevated CO2 on the partitioning of N; (ii) traced immobilized N into physically separated pools of soil organic matter (SOM) with turnover rates known from their 13C signals; and (iii) estimated the remobilization and thus, the bio-availability of newly sequestered C and N. (1) CO2 enrichment significantly decreased NO3− concentrations in soil waters and export from 1.5 m deep lysimeters by 30–80%. Consequently, elevated CO2 increased the overall retention of N in the model ecosystems. (2) About 60–80% of added 15NH415NO3 were retained in soils. The clay fraction was the greatest sink for the immobilized 15N sequestering 50–60% of the total new soil N. SOM associated with clay contained only 25% of the total new soil C pool and had small C/N ratios (<13), indicating that it consists of humified organic matter with a relatively slow turn over rate. This implies that added 15N was mainly immobilized in stable mineral-bound SOM pools. (3) Incubation of soils for 1 year showed that the remobilization of newly sequestered N was three to nine times smaller than that of newly sequestered C. Thus, inorganic inputs of N were stabilized more effectively in soils than C. Significantly less newly sequestered N was remobilized from soils previously exposed to elevated CO2. In summary, our results show firstly that a large fraction of inorganic N inputs becomes effectively immobilized in relative stable SOM pools and secondly that elevated CO2 can increase N retention in soils and hence it may tighten N cycling and diminish the risk of nitrate leaching to groundwater.