Iron (Fe) and manganese (Mn) are crucial for sustaining ecosystem productivity by regulating soil microbial structure and function, while the factors influencing the transformation and dynamics of Fe and Mn during succession, particularly in subalpine forests with seasonal freeze–thaw cycles and acidic soils, are not well understood. Therefore, we investigated the effects of both abiotic and biotic factors on Fe and Mn dynamics (with a soil depth of 0–20 cm) in subalpine secondary succession, progressing from grassland to shrubland, then to secondary forest, and finally to primary forest. The objectives were to clarify the changes in Fe and Mn contents and their drivers during vegetation succession. Phospholipid fatty acid (PLFA) was used to analyze microbial community, and variance partitioning analysis (VPA) analyzed the relative contribution of abiotic and biotic factors on Fe and Mn dynamics. VPA showed that the contents of Fe2+ and Fe oxides were mainly affected by abiotic factors (61 %), whereas biotic factors had a negligible influence (1.3 %). Soil pH, moisture, and redox potential were the important abiotic factors affecting Fe dynamics during vegetation succession. In contrast, Mn contents were more influenced by biotic (9.4 %) than abiotic factors (2.7 %) by VPA. Arbuscular mycorrhizal fungi, gram-positive and negative bacteria were the key biotic factors regulating Mn contents by uptake of Mn2+ and secreting organic acids such as citric acid. Consequently, the relative influence of abiotic and biotic factors on Fe and Mn dynamics advances both the understanding of ecosystem productivity and ecosystem restoration management in alpine regions.