The seed composition of four varieties of Opuntia ficus-indica growing in Algeria was investigated. Seeds ground into a fine powder were first, subjected to oil extraction and fatty acids analysis. The phenolic compounds were then extracted from the defatted powder of seeds in order to be quantified and characterised by liquid chromatography coupled to mass spectrometry (LC-MSn) and to nuclear magnetic resonance (LC-NMR) approaches. In addition, an evaluation of the antioxidant activity of the phenolic extracts was investigated. Gas chromatography analysis of the seed oil showed high percentages of linoleic acid in the four varieties ranging from 58% to 63%. The phenolic profile of the Opuntia ficus-indica seeds displayed a high complexity, with more than 20 compounds detected at 330 nm after the LC separation. Among them, three isomers of feruloyl-sucrose were firmly identified and another was strongly supposed to be a sinapoyl-diglycoside. High correlations were found between phenolic content in the defatted seed extracts and their antioxidant activity. The data indicate that the defatted cactus seed wastes still contain various components that constitute a source for natural foods.