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Acyl activating enzyme 3 (AAE3) was identified as being involved in the acetylation pathway of oxalate degradation, which regulates the responses to biotic and abiotic stresses in various higher plants. Here, we investigated the role of <i>Glycine soja</i><i>AAE3</i> (<i>GsAAE3</i>) in Cadmium (Cd) and Aluminum (Al) tolerances. The recombinant GsAAE3 protein showed high activity toward oxalate, with a <i>K_m</i> of 105.10 ± 12.30 μM and <i>V_max</i> of 12.64 ± 0.34 μmol min⁻¹ mg⁻¹ protein, suggesting that it functions as an oxalyl–CoA synthetase. The expression of a GsAAE3–green fluorescent protein (GFP) fusion protein in tobacco leaves did not reveal a specific subcellular localization pattern of <i>GsAAE3</i>. An analysis of the <i>GsAAE3</i> expression pattern revealed an increase in <i>GsAAE3</i> expression in response to Cd and Al stresses, and it is mainly expressed in root tips. Furthermore, oxalate accumulation induced by Cd and Al contributes to the inhibition of root growth in wild soybean. Importantly, <i>GsAAE3</i> overexpression increases Cd and Al tolerances in <i>A. thaliana</i> and soybean hairy roots, which is associated with a decrease in oxalate accumulation. Taken together, our data provide evidence that the <i>GsAAE3</i>-encoded protein plays an important role in coping with Cd and Al stresses.