Milk thistle is a plant that perfectly meets the needs of sustainable agriculture. Despite their high protein content, the seeds and endosperm of S. marianum have not been considered as raw food material so far. Therefore, the work aimed to characterize milk thistle endosperm in terms of its possible use in producing novel food. The nutritional and energy value of the raw material, profile of amino acids), fatty acids, and health quality indices of lipids were characterized. The main components of milk thistle endosperm (MTE) were protein (>20% dry matter (DM)), fat (>39% DM), and fiber (>31% DM). MTE protein is characterized by a high content of sulfur, aromatic amino acids, and tryptophan, comparing the FAO/WHO patterns. The PDCAA S (Protein Digestibility Corrected Amino Acid Score) value for lysine is low but can be higher in combination with other proteins. Milk thistle fat is dominated by unsaturated fatty acids, constituting about 80% of total fatty acids, of which over 56% are polyunsaturated fatty acids. Low values of atherogenicity and thrombogenicity indices of MTE fat testify to its potentially beneficial properties towards the cardiovascular system.