Optimal transitions have been selected for the identification and quantitation of the most interesting hydrophilic biophenols in extracts from olive-tree materials, which are of interest because of their nutraceutical properties. The tested materials were extra virgin olive oil, waste from oil production (known as alperujo), and olive-tree materials such as leaves, small branches and fruit stones. The identification and determination steps of the target biophenols are based on liquid chromatography/tandem mass spectrometry (LC/MS/MS) with a triple quadrupole (QQQ) mass detector. The interface between the chromatograph and the QQQ was an electrospray ionization source operated in the negative ion mode. Highly selective identification of the biophenols was confirmed by multiple reaction monitoring (MRM) using the most representative transitions from the precursor ion to the different product ions. Quantitative MS/MS analysis was carried out by optimization and selection of the most sensitive transition for each analyte, which resulted in estimated detection limits of 5.10 to 11.65 ng/mL for the extracts. The biophenols were extracted from the tested samples by different methods: liquid-liquid extraction for virgin olive oil, microwave-assisted leaching for olive leaves, branches and stones, and pressurized liquid leaching for alperujo. This study provides valuable information about the most suitable source for the isolation of each nutraceutical biophenol and enables us to obtain a complete profile of them in Olea Europaea.