The adoption of two-phase olive oil extraction processes has led to a significant increase in the amounts of two-phase olive pomace produced each year. This material is typically led to kernel oil extraction facilities that are forced to store the excessive amounts until treatment. During storage, malodorous compounds, like 4-ethylphenol, are formed that are then released to the atmosphere during drying, causing serious problems in a radius of several kilometers. At the same time, increased microbial activity in the stored pomace deteriorates kernel oil, diminishing its value. This deterioration is expressed as increased kernel oil acidity. In this work, the evolution of 4-ethylphenol concentration and kernel oil acidity as a function of storage duration and waste acidification were examined. The concentration of 4-ethylphenol in the unmodified two-phase olive pomace seems to be maximized after 23 d of storage, while kernel oil acidity reached a plateau of 10% after 70 d. Acidification at pH 2 prevented the production of 4-ethylphenol and kept kernel oil acidity at 5% for more than 100 d of storage. The results presented herein are a step towards understanding the processes taking place during two-phase olive pomace storage and exploring ways of minimizing their effects.