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Second-generation biofuel crop miscanthus is one of the most promising plants tested for phytomanagement of contaminated sites. In this preliminary pot case study, the most used hybrid Miscanthus x giganteus was cultivated in three different real contaminated soils: agricultural soil contaminated with Cd, post-military soil slightly contaminated with Zn, Pb and Cd, and soil contaminated by petroleum industry with metals and hydrocarbons. The stress response of plants and soil microbial communities was monitored to receive data that are important for successful phytomanagement application. With metals only, the plant grew well, and chlorophyll fluorescence measurement proved their good vitality. Changes in leaf anatomy (leaf thickness and sclerenchyma cells area) were additionally determined in post-military soil compared to agricultural. On the contrary, in petroleum-contaminated soil, the biomass yield was too reduced and also physiological parameters were significantly decreased. The response of microbial communities also differed. In agricultural soil, no microbial stress was determined. In post-military soil, it became reduced during the experiment, and in petroleum contamination, it increased year-on-year. It could be concluded that miscanthus is suitable for cultivation in metals contaminated soils with potential for microbial communities support, but in soil contaminated by the petroleum industry, its application did not seem meaningful.