Gluten-free flours are interesting alternative to wheat flours. They could be by-products of oilseed processing, characterized by high content of bioactive compounds. Therefore the aim of the study was to determine the antioxidant, antimicrobial properties, amino acid and fatty acid profile of flours obtained as by-products from the oil industry. The highest total polyphenol content and antioxidant activity was found to have evening primrose flour. The widest spectrum of microbial growth inhibition was indicated for corn germ extract which showed no antimicrobial activity only against Bacillus subtilis. The highest protein content was found in pumpkin, peanut and almond flours (more than 50 g/100 g). The major abundant amino acids in all the analysed oilseed cake flours were aspartic acid, glutamic acid and arginine. The analysed gluten-free flours were found to be a good source of polyunsaturated fatty acids (PUFAs), which comprised mainly linoleic acid and α-linolenic acid, whereas the best source of PUFAs was evening primrose flour. The results suggest that the cold-pressed seed flours possess valuable chemical composition and may be considered for improvement of the nutritional properties of food products.