Over the last decade, the two-phase centrifugation system for olive-oil extraction has become dominant in Slovenia. There are many suggestions for the exploitation of two-phase OMW, but among the suggested methods, direct spreading on agricultural land appears to be operationally simple and economically feasible for Slovenia. As there is little information available about two-phase OMW produced in the northern Mediterranean regions, the aim was to determine its composition and evaluate its use as a soil amendment in olive groves. This study shows that the characteristics of two-phase olive-mill waste produced in northern Mediterranean regions are similar to those of other countries. In addition, the calcareous characteristics of the Mediterranean soil can reduce its phytotoxic effects and might thus represent a natural system for olive-mill waste treatment. Phenolic compounds in the two-phase olive-mill waste are rapidly decomposed, and the soil has a high buffering capacity. Furthermore, the results of the soil analysis also showed some effects on the soil properties, such as a significant increase in K2O and soil organic carbon. The combined application of two-phase olive-mill waste and mineral fertilizer to olive groves on eutric cambisols has positive effects on the physical, chemical and biochemical properties of the soil.