Phytochemical compounds have been associated with possible beneficial health effects. Therefore, many studies have been conducted in order to identify and quantify these compounds of interest. Given the characteristics of different methods, it is critical to choose the suitable one to attain high-quality data within a minimum acquisition time. In this regard, the state of the art of phytochemical investigation from extraction and cleaning (or purification), separation techniques to the final analysis are discussed. Chromatographic techniques hyphenated with high-resolution mass spectrometry are powerful tools that are being increasingly used in recent years. In the same way, nuclear magnetic resonance and infrared spectroscopy (NIR, MIR, and FTIR) are fast, non-destructive and accurate methods used to quantify polyphenols, carotenoids, and fatty acids. Finally, selected studies are presented and the analysis of phenolic compounds in apples is discussed.