The amino acids profiles of tomato and strawberry juices subjected to high intensity pulsed electric fields (HIPEF) treatment were evaluated and compared to those of thermally treated juices. Both HIPEF and thermal treatments (TT) depleted the initial content of total free amino acids of tomato juice. However, HIPEF-treated juices exhibited higher concentration (769 mg/L) than thermally treated juices (750 mg/L). HIPEF treatment enhanced the concentration of phenylalanine (27%), glutamic acid (6.8%), valine (6.3%), serine (5.5%) and alanine (4.8%), and in turn, the total free amino content of strawberry juice. In contrast, TT caused a reduction in the content of most amino acids compared to fresh juice. Although total free amino acids in treated tomato juice were substantially enhanced during storage, the content of some minor amino acids (proline, leucine, valine, isoleucine, arginine, lysine, phenylalanine and methionine) decreased over time. Regarding strawberry, HIPEF-treated juices exhibited higher amino acid content than thermally treated juices during storage. Individual and total amino acid concentrations increased during the storage, except for leucine concentrations, which significantly decreased (23%) with time. Hence, HIPEF could be considered a potential preservation and processing method to obtain shelf-stable fruit juices with high nutritional value.