The oil industry generates great quantities of oilseed cakes that remain after oil extraction. New technologies are required for their valorization, owing to their high nutritional value. Pumpkin, flax and hemp seed cakes were extracted by subcritical water under different conditions that included different gas atmospheres and homogenous catalysis, and for the first time their properties were directly compared. Extracts obtained in a nitrogen atmosphere, nitrogen atmosphere with the addition of a catalyst, and carbon dioxide atmosphere were chemically and nutritionally characterised. In the aqueous extracts obtained under different extraction conditions, the content of lipids, proteins and selected minerals (calcium, potassium, sodium and phosphorus) were determined. A detailed amino acid profile was determined by chromatographic analysis. The highest relative content of essential amino acids was observed in pumpkin seed extracts (51.49 ± 0.47 to 58.58 ± 0.45 mg/100 g dry extract), whereas hemp seed extracts were the richest in flavour amino acids aspartic acid, glutamic acid and alanine. Extraction in a carbon dioxide atmosphere or in nitrogen atmosphere with a HCl modifier released generally more minerals into the aqueous phase. Aqueous oilseed cake extracts demonstrated a favorable chemical composition and great nutritional value, opening new possibilities for exploitation of this biowaste. Based on the obtained results, oilseed cake extracts obtained by subcritical water have great potential to be used for the fortification of different food products, as well as in cosmetics.