The association of soil organic matter (SOM) with iron (Fe) oxides by adsorption and/or co-precipitation contributes to long term C stabilization in soil. While there is an understanding of the relationship between soil carbon (C) and the biogeochemical cycling of Fe, a lack of information exists on the role of Fe oxides on the accumulation of C in paddy soils. This study aimed to assess the role of Fe (oxyhydr)oxides on mineralization and stabilization processes following amendment of paddy soil with a labile C substrate (99 atom % 13C-glucose). The study utilized 4 paddy soils with a total Fe concentration ranging from 13.7 to 55.8 g kg−1. In soils with 42.7 and 55.8 g kg−1 Fe, the addition of glucose resulted in an Fe bound organic C: Fe molar ratio (C:Fe molar ratio) ≥6, suggesting the formation of Fe-OM complexes mainly via co-precipitation. The highest portion of 13C (13.8%) protected in Fe-OM complexes was found in soil containing 55.8 g kg−1 of Fe. The stabilization of the added labile C substrate was shown, using random forest analysis, to be controlled by the C: Fe molar ratio, while substrate mineralization was regulated by the core genera Sphingomonas and Devosa (r-strategists) (affiliated to Proteobacteria) and C:N ratio. Substrate mineralization was 47% lower in soil containing 55.8 g Fe kg−1 compared to 13.7 g Fe kg−1, with a concomitant reduction in SOM priming of 37%. This reduction in substrate mineralization and the priming effect was likely due to lower C substrate availability via the formation of Fe-OM complexes, thereby protecting the C from mineralization. In conclusion, the Fe concentration in paddy soils plays a central role in the abiotic stabilization of ‘new’ C through the formation of Fe-OM complexes via co-precipitation, thereby limiting the availability of this C substrate for microbial mineralization, and at the same time modulating the microbial community structure.