The effect of olive stone removal before processing on the degradation level, secoiridoid and tocopherol contents, and antioxidant activity of monovarietal extra virgin olive oils (EVOOs) was studied. EVOOs were extracted from olives of the Leccino, Moraiolo, Frantoio, Pendolino, Taggiasca, and Colombaia varieties both in the presence and in the absence of the stones. The degradation level of EVOOs was evaluated by acidity, peroxide number, and spectroscopic indices K(232) and K(270), according to EU regulation. The secoiridoid compounds typical of EVOO, namely, the oleuropein and ligstroside derivatives, hydroxytyrosol, tyrosol, and tocopherols were analyzed by HPLC. The antioxidant activity was evaluated by the xanthine oxidase/xanthine system, generating superoxide radical and hydrogen peroxide, and by the 2,2-diphenyl-1-(2,4,6-trinitrophenyl)hydrazyl test. Results showed that EVOOs obtained from both stoned and destoned olives had a very low degradation level, which was not affected by destoning. Destoning lowered slightly the alpha-tocopherol content in EVOOs but increased the total secoiridoid content and the antioxidant activity of EVOOs (up to 3.5-fold). However, these effects were variety-dependent and negligible in some conditions. It was concluded that a better knowledge of the reactions occurring during olive processing, and particularly on the involvement of endogenous pulp and stone enzymes, is essential to predict the effect of destoning on EVOO quality.