Natural wetlands are mostly nitrogen-limited ecosystems, while reclamation stimulates the loss of nitrogen (N) in soils by shifting the N regime. To investigate the microbial mechanisms of the N regime shift, we first conducted a global meta-analysis to quantify the wetland reclamation impacts on soil mineral N pools and then a field campaign to sample 24 soil cores up to 100 cm depth in a natural wetland and a 23-year cultivated soybean field from the Sanjiang Plain in northeastern China. After wetland reclamation, the N regime was shifted to cause a potential risk of massive N loss in soils; their microbial mechanisms were revealed through metagenomic data. In cropland, the relative abundance of genes involved in nitrification and assimilatory nitrate reduction to ammonia (ANRA) were enriched while those in N fixation, mineralization, denitrification, and dissimilatory nitrate reduction to ammonia (DNRA) were diminished. Wetland reclamation substantially enhanced the relative abundance of genes involved in nitrification (except for genes for ammonia oxidation to NH₂OH) and denitrification in surface (0–30 cm) soils but decreased them in subsurface (30–100 cm) soils. After wetland reclamation, the relative abundance of genes involved in denitrification and DNRA significantly reduced in spring and summer, but such patterns were not found in autumn and winter. This change enhanced potential microbial-driven N loss in spring and summer. The metagenomic data serve as surrogate data sources for quantifying soil roles on soil N cycles under land use change.