The impact of two- and three-phase processing systems and malaxation conditions on phenol content (both total and individual phenols) and antioxidant capacity of laboratory-generated olive mill waste (OMW) were assessed. Two-phase olive processing generated a waste with higher phenol content and antioxidant capacity. Using the two-phase system both malaxation time and temperature affected the phenol content and antioxidant capacity. The effects of different pre-storage drying treatments on phenol content and antioxidant capacity were also compared. Air drying and drying at 60 °C resulted in a substantial decrease in the phenol content and antioxidant capacity. Drying at 105 °C and freeze-drying produced less degradation. Changes in the phenol content and antioxidant capacity of OMW stored at 4 °C, and OMW preserved by 40% ethanol w/w and 1% acetic acid w/w and stored at 4 °C were monitored for 30 days and compared with OMW stored at room temperature. None of these storage conditions could stop the fast decrease in phenolic concentrations and antioxidant capacity, which happened within the first 24 hours.