Abstract Anaerobic ammonium oxidation coupled to iron reduction, termed Feammox, is a new microbial process linked the nitrogen cycles. However, the nitrogen losses through Feammox from different ecosystem habitats remain unclear. In this study, isotope tracing technology and molecular microbial analysis were used to investigate the Feammox and its contribution to the nitrogen loss in the farmland and riparian soils, and river sediments. The potential Feammox rates were detected, which varied from 0.07 to 0.15 mg N kg−1 d−1 among the three ecosystem habitats. Feammox rates were significantly higher in the farmlands or riparian soils than in the river sediments. Feammox, denitrification and anaerobic ammonium oxidation (anammox) were estimated to account for approximately 3.5–4.2%, 92.6–93.1% and 2.8–3.9% of the total nitrogen losses respectively, while a significant correlation was observed between the Feammox rates and the denitrification rates (r = 0.72, P < 0.05). In addition, a nitrogen loss at 8.3–17.8 kg N ha−1 yr−1 was linked with Feammox in the examined soils. This study demonstrated that Feammox could be a potential pathway of nitrogen loss from ecosystem habitats. Graphical abstract Unlabelled Image Highlights • Nitrogen losses by Feammox were higher in farmland soils than in river sediments. • Denitrification was the major pathway of nitrogen losses in the natural ecosystems. • There was a significant correlation between Feammox and denitrification rates. • Soil moisture is an important factor affecting the potential rates of Feammox. [ABSTRACT FROM AUTHOR]