Ecological engineering of Fe-ore tailings into Technosols (or soil-like growth media) offers a promising way to rehabilitate tailings without resorting to natural topsoil from other places. Among key pedogenic processes, soil aggregate formation and organic matter (OM) stabilisation are critical to the development of sustainable Technosols. The colonisation of pioneer plant species highly adaptive to infertile soils and water deficit may act as competent biological drivers to enhance these critical processes involved in Technosol formation. This study aimed to investigate the role of an Australian native plant species, Acacia auriculiformis, in enhancing water-stable aggregate formation and associated OM stabilisation using a pot experiment under glasshouse conditions. With water deficit and phosphorus deficiency under field conditions, two relevant abiotic processes and their influence on these key processes have also been evaluated. A. auriculiformis colonisation enhanced the formation of water-stable aggregates in the early Technosols, while the proportion of macroaggregates and microaggregates were altered differently, with the former increasing under well-watered conditions and the latter increasing under water deficit conditions. A. auriculiformis colonisation enriched N-rich OM associated with minerals within the macroaggregates. In aggregates, OM stabilisation was related to interactions of carboxyl-rich organic groups with tailing minerals. The influences of water deficit and phosphorus deficiency on aggregate formation and OM stabilization were mediated via their impacts on the growth and root functions of A. auriculiformis, including root extension, entanglement, and exudation. From these findings, the utilization of A. auriculiformis is recommended as a biological driver to facilitate the development of early Technosols from eco-engineered Fe-ore tailings.