Long-term field experiments were performed to evaluate the phytotoxic properties of fungal metabolites in oil-contaminated soil and to assess the impact of contamination on the allelopathic activity of soil mycobiota. Two contrasting soils of Northwest Russia (sandy and loamy podzols) exposed to oil contamination underwent changes in abundance and allelopathic activities of soil fungi. Shifts within the microbial community caused by oil contamination affected not only oil-decomposition rates but also ecotoxicity of contaminated soil. There were significant differences in soil toxicity dynamics between sandy and loamy podzols. Four years after contamination, ecotoxicity of loamy podzol decreased, whereas sandy podzol remained highly toxic even nine years after contamination. The abundance and allelopathic activity of fungi is correlated with hydrocarbon degradation dynamics. The soil fungal community demonstrated high allelopathic activity which decreased over time in fertile loamy podzolic soil, whereas in poor sandy podzolic soil it remained high over the nine-year monitoring period. The results illustrate how oil contamination may influence allelopathic interactions in soil and demonstrate the advantage of using fungal metabolite toxicity test for testing of oil-contaminated soil samples.