The chemical properties, ecotoxicity, and microbiome of leachates from phytomanaged Cu-contaminated soils were analyzed. The phytomanagement was carried out using Cu-tolerant poplar Populus trichocarpa × deltoides cv. Beaupré and black bent Agrostis gigantea L., aided by soil amendments, i.e., dolomitic limestone (DL) and compost (OM), alone and in combination (OMDL). Plants plus either DL or OMDL amendments reduced in leachates the electrical conductivity, the Cu concentration, and the concentration of total organic C except for the OMDL treatment, and decreased leachate toxicity towards bacteria. Total N concentration increased in the OM leachates. The aided phytostabilization increased the culturable bacteria numbers and the proportion of Cu-resistant bacteria in the leachates, as compared to the leachate from the untreated soil. Phytomanagement also enriched the microbial communities of the leachates with plant beneficial bacteria. Overall, the Cu stabilization and phytomanagement induced positive changes in the microbial communities of the soil leachates.