Display omitted •Cooking methods for quinoa and buckwheat do not affect amino acid profile.•Malting process affects the amino acid content and profile of pseudocereals.•Retention values for most amino acids increased significantly in malted samples. This study reports the effect of boiling, steaming and malting on the amino acid composition of the pseudocereals amaranth, buckwheat and quinoa. For all pseudocereals the foremost amino acid was glutamic acid, presenting 13.2% in both raw and malted (2.2 g/100 g), and 15.6% in steamed (2.5 g/100 g) amaranth; 10.8% in steamed (2.0 g/100 g) and 17.6% in boiled (2.1 mg/100 g) quinoa; 15.4% in malted (2.3 g/100 g) and 21.2% in raw (2.8 g/100 g) buckwheat. Almost all amino acids present in the three pseudocereals evinced a significant increase of the retention values in malted samples, except in amaranth and quinoa for cysteine and glutamic acid, respectively. Histidine and aromatic amino acids presented the highest values of amino acid scores. Cluster analysis allowed to identify the pseudocereals with the highest nutritional protein quality, were boiled and malted quinoa and raw and malted buckwheat were included. Malting process revealed to be the method that produce more effect on the amino acid content for all pseudocereals.