Olive mill wastewaters (OMW) resulting from the extraction of olive oil possess high organic loads and elevated contents in phenolic compounds, which are usually toxic and recalcitrant to biological wastewater treatments. In this work, a strain of Candida oleophila isolated from olive wastewaters was used for biological detoxification treatments of OMW samples. The effect of treatment with this isolate was evaluated by using germination tests, bioluminescence assays, and studies on mitochondrial bioenergetics. Incubation with the C. oleophila isolate was able to remove about 50% of the organic load, and 83% of total polyphenol content, from undiluted and non-supplemented OMW samples. Germination tests confirmed the reduction of toxicity of the treated effluent since when using diluted and treated OMW the germination index increased up to 32% when compared to the values obtained with untreated water. Treated OMW also decreased antimicrobial activity in about 50% as confirmed by the bioluminescence inhibition assay. Significant effects were also observed in mitochondrial bioenergetics. A decrease of toxicity toward two respiratory complexes, namely succinate dehydrogenase and ATPase, was recorded when using treated OMW. Overall, this C. oleophila isolate was able to remove organic matter and decrease toxicity of OMW effluents, showing promising abilities for future application in biological treatments.