A sustainable practice for weed control and crop protection is the incorporation of green manures with phytotoxic potential. It is gaining attention as a way to reduce the use of synthetic herbicides in agriculture and so pot experiments and field trials were conducted to explore the possible use of residues of Acacia species to alleviate weed emergence. We assessed, under greenhouse conditions, the herbicidal effect of phytotoxic manures from Acacia dealbata and Acacia longifolia applied to soil at different doses (1.5 and 3% w/w) on maize growth, some accompanying weeds, and the physiological profile of soil microbes. Applied at a higher dose, A. dealbata residues reduced the emergence of dicotyledons in the short-term (P < 0.05) and, after 30 days, there was a decrease in total weed emergence (P < 0.005) and a mild effect on weed composition, while total weed biomass remained unaffected. Regardless of the inclusion of Acacia residues, the physiological profile of the soil bacterial community did not show significant alterations. Additionally, we tested A. dealbata residues as a mulch or a green manure at the field scale. Although the effects of manures were site-dependent and affected monocot and dicot weeds differentially, dicots were more sensitive. The herbicide potential of acacia residues was only evident for dicots at sites with low-weed density in the seed bank. Nevertheless, due to the absence of phytotoxic effects on maize and minor modifications in the functional profile of bacterial communities, residues of acacia could be used as a complementary tool used together with other practices to reduce the reliance on synthetic herbicides in maize-based cropping systems.