The phenolic composition of Cynara cardunculus L. var. altilis (DC) from south of Portugal was determined by analyzing the methanol/water/acetic acid (49.5:49.5:1) extracts of the different morphological parts of the plant, through high temperature-ultra high pressure liquid chromatography–tandem mass spectrometry. From the twenty-eight phenolic compounds identified, eriodictyol hexoside was described for the first time in C. cardunculus L., and 1,4-di-O-caffeoylquinic acid, naringenin 7-O-glucoside, naringenin rutinoside, naringenin, luteolin acetyl-hexoside and apigenin acetyl-hexoside as cardoon components. Stalks outer part and capitula florets showed the highest hydroxycinnamic acids and flavonoids contents, respectively. Capitula receptacle and bracts, and stalks inner part also presented considerably high hydroxycinnamic acids contents, while leaves were rich in flavonoids. Finally, stalks outer part and capitula receptacle and bracts extracts showed the highest antioxidant activity which was in perfect tune with the phenolic compounds, particularly to hydroxycinnamic acids. These results clearly demonstrate the potential of this crop as a source of antioxidant phenolic compounds.