Labile organic matter (OM) immobilized by secondary iron (Fe) minerals from chemodenitrification may be an effective way to immobilize organic carbon (OC). However, the underlying mechanisms of coupled chemodenitrification and OC sequestration are poorly understood. Here, OM immobilization by secondary Fe minerals from chemodenitrification was investigated at different C/Fe ratios. Kinetics of Fe(II) oxidation and nitrite reduction rates decreased with increasing C/Fe ratios. Despite efficient sequestration, the immobilization efficiency of OM by secondary minerals varied with the C/Fe ratios. Higher C/Fe ratios were conducive to the formation of ferrihydrite and lepidocrocite, with defects and nanopores. Three contributions, including inner-core Fe-O and edge- and corner-shared Fe-Fe interactions, constituted the local coordination environment of mineral-organic composites. Microscopic analysis at the molecular scale uncovered that labile OM was more likely to combine with secondary minerals with poor crystallinity to enhance its stability, and OM distributed within nanopores and defects had a higher oxidation state. After chemodenitrification, high molecular weight substances and substances high in unsaturation or O/C ratios including phenols, polycyclic aromatics, and carboxylic compounds exhibited a stronger affinity to Fe minerals in the treatments with lower C/Fe ratios. Collectively, labile OM immobilization can occur during chemodenitrification. The findings on OM sequestration coupled with chemodenitrification have significant implications for understanding the long-term cycling of Fe, C, and N, providing a potential strategy for OM immobilization in anoxic soils and sediments.