Dry olive residue (DOR), a solid by-product of the two-phase olive oil extraction system, is rich in organic matter and nutritionally important compounds. However, the agronomic application of this residue may impact negatively on the soil ecosystem due to its toxic components. The aim of the present studywas to investigate the impact of raw DOR, Coriolopsis floccosa-transformed DOR and Fusarium oxysporum-transformed DOR on soil biological properties. To do this, soil enzyme activities, fungal community size (quantitative PCR) and fungal community structure (DGGE of 18S rRNA gene) were measured. The impact of biotransformed and nonbiotransformed DOR applications to soil depended on two factors: the variable sensitivity of the soil to the residue’s composition and the duration of exposure to amendments. The application of this biotransformed residue enhanced soil enzyme activities (phosphatase, b-glucosidase and urease) with respect to soil amended with nonbiotransformed residue. The quantification of the 18S rRNA gene copy number indicated that the different amendments stimulated relative abundance. DGGE analysis showed that the amendments produced changes in fungal community structure although variations in fungal diversity were only detected after C. floccosa-transformed DOR addition at 60 days,probably due to the enhancement of species such as Chaetomium globosum and Chalazion helveticum.