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The literature data concerning the qualitative and quantitative alterations of olive key metabolites during the process of olive oil production are often contradictory and it seems that the parameters, such as the production procedure, the variety, the origin, the harvesting season, and so forth, play a crucial role. However, in spite of the existent discrepancies in the literature, it seems that there are specific trends followed by bioactive molecules during olive oil production that are accepted by the majority of researchers. It is a fact that from all molecules, even the more lipophilic ones, such as the triterpenic acids, only a small percentage ends up in the olive oil. In the three-phase systems, most of the valuable constituents are lost in the waste water. In the two-phase olive mills, a greater percentage of biophenols is lost in the solid wastes and the final product contains only a small portion of secoiridoids …