The research was aimed at determining the efficiency of phytoremediation supported by bioaugmentation using a microbial consortium based on autochthonous bacteria and wild plants naturally growing in an area of natural petroleum seeps (Scirpus sylvaticus and Cirsium oleraceum),transplanted for the cleanup of hydrocarbon-contaminated soil. A six-month phytoremediation process resulted in a decrease in concentrations: TPH—from 4320 to 455–261 mg/kg dry mass, and PAHs—from 7.19 to 1.47–1.76 mg dry mass. The greatest reductions were observed for (91.9–99.8 %) and naphthalene (85.3–87.4 %), and the lowest for (62.0–87.3 %) and 4–6-ring PAHs (44.0–76.3 %). Intense growth of roots and shoots was found in plants from bioaugmented soils. Toxicological studies performed using biotests with varying sensitivity (Ostracodtoxkit < Microtox < MARA) and phytotoxicity test (Phytotoxkit) indicated a decrease in toxicity levels after phytoremediation supported by bioaugmentation, which correlated with the drop in TPH and PAHs contents in the treated soil. The study also evaluated the structure of the microbial community in the remediated soil. The presence of bacteria in the rhizosphere accelerated the degradation of contaminants and increased plant tolerance to adverse environmental conditions. Additionally, changes in the community of soil ciliates were assessed, showingthat functional group responses, rather than species richness alone, may serve as sensitive indicators of soil recovery and ecological stability. This study highlights the novelty and ecological relevance of combining wild-adapted plants and microbial consortia for sustainable remediation, while also demonstrating the potential of ciliates as sensitive bioindicators of soil recovery.