The effect of the use of cell-wall-degrading-enzyme preparations during the mechanical extraction process of virgin olive oil on the phenolic compounds and polysaccharides was investigated. The use of the enzyme preparations increased the concentration of phenolic compounds in the paste, oil, and byproducts. Especially, the contents of secoiridiod derivatives such as the dialdehydic form of elenolic acid linked to 3,4-dihydroxyphenylethanol (3,4-DHPEA-EDA) and an isomer of oleuropein aglycon (3,4-DHPEA-EA), which have high antioxidant activities, increased significantly in the olive oil. Furthermore, the use of an N2 flush during processing strongly increased the phenolic concentration. Analyses of the pectic polymers present in the paste showed that the use of pectinolytic enzyme preparations increased the yield of the buffer soluble pectins and the proportion of molecules with a lower molecular mass. Also, the content of uronic acids in the buffer soluble extract increased considerably due to the use of the enzyme preparations. Analysis of the polymeric carbohydrates in the vegetation waters showed the presence of mainly pectic polymers. The addition of commercial enzyme preparations increased the uronic acid content of the polysaccharides in the vegetation water substantially compared to the blank. This study showed that the addition of cell-wall-degrading enzymes did improve the olive oil quality; however, mechanisms remained unclear.