Electrolytic manganese residue (EMR), due to its large-scale storage, contains high concentrations of manganese (Mn) and ammonium nitrogen ( \({\text{NH}}_{4}^{ + }\) -N), posing a severe threat to the environment and human health with its poor physicochemical properties. The combination of amendments and phytoremediation represents an cost-effective approach for EMR management. This study investigates the effects of amendments on mitigating the harsh conditions of EMR and their influence on phytoremediation. Under non-closed greenhouse conditions, potting experiments lasting 60 days were conducted, incorporating different ratios of activated phosphorus tailings and mature sludge as amendments into EMR, alongside Lolium perenne L., Medicago sativa, and Cynodon dactylon. Results indicate that the application of amendments significantly improved the properties of EMR, optimizing plant growth conditions. Mn and \({\text{NH}}_{4}^{ + }\) -N became more stable, reducing their concentrations and bioavailability in leachate. Moreover, Mn content in plant roots and shoot markedly decreased, while the activities of glutamate synthase (GOGAT), glutamine synthetase (GS), and glutamate dehydrogenase (GDH) were significantly enhanced. In summary, amendments not only effectively improved the habitat quality of EMR but also increased the tolerance of remediation plants to Mn and \({\text{NH}}_{4}^{ + }\) -N, demonstrating potential in EMR remediation.