Extra-virgin olive oil (EVOO) is largely appreciated for its proven nutritional properties. Additionally, organic foods are perceived as healthier by consumers. In this context, the aim of the present study was to compare the phenolic profiles of EVOO from olives of the Hojiblanca variety, cultivated under organic and conventional systems. The quantification and identification of individual polyphenols was carried out by liquid chromatography coupled to mass spectrometry in tandem mode (LC-MS/MS). Significantly higher levels (p < 0.05) of phenolic compounds were found in organic EVOOs. The methodology used was able to detect previously unreported differences in bioactive components between organic and conventional EVOOs.