Organic amendments are commonly used in assisted phytostabilization of mine wastes by improving their physicochemical and biological properties. These amendments are susceptible to leaching and degradation, resulting in the generation of dissolved organic matter (DOM), which significantly influences the geochemical behaviour of heavy metals (HMs). However, the geochemical behaviour of HMs in metal smelting slag driven by organic amendment-derived DOM remains unclear. In this study, we investigated the impact of cow manure-derived DOM on the release behaviour, bioavailability, and speciation of HMs (Cu, Pb, Zn, and Cd) in zinc smelting slag using a multidisciplinary approach. The results showed that DOM enhanced the weathering of the slag, with a minimal impact on the slag’s mineral phases, except for causing gypsum dissolution. The DOM addition resulted in a slight increase in HM release from the slag during the initial inoculation period, followed by a reduction in HM release during the later period. Furthermore, the DOM addition increased the diversity and relative abundance of the bacterial community. This, in turn, led to a decrease in the dissolved organic carbon (DOC) content and enhanced the transformation of labile DOM compounds into recalcitrant compounds. The variation in HM release during various inoculation periods can be attributed to the bacterial decomposition and transformation of DOM, which further enhanced the transformation of HM fractions. Specifically, during the later period, DOM promoted the conversion of a portion of the reducible and oxidizable fractions of Cu, Pb, and Zn into the acid-soluble and residual fractions. Moreover, it partially transformed the reducible, oxidizable, and residual fractions of Cd into the acid-soluble fraction. Overall, this study provides new insights into the geochemical behaviour of HMs in slag governed by the coupling effect of DOM and the bacterial community. These findings have implications for the use of organic amendments in assisted phytostabilization of metal smelting slag. Environmental implicationMetal smelting slag is hazardous due to its high levels of HMs, and its improper disposal has serious consequences for the ecosystem. Organic amendments are employed in assisted phytostabilization of the slag site by improving its microecological properties. However, the impact of organic amendment-derived DOM on HM migration and transformation in slag remains unclear. This study indicated that the coupling effects of DOM and microbes governed the geochemical behaviour of HMs in slag. These findings provide new insights into how organic amendments impact the geochemical behaviour of HMs in slag, contributing to the development of phytostabilization technology.