High pressure (HP) is a non-thermal treatment that is generally used to reduce the microbiological contamination of food products, such as Atlantic salmon (Salmo salar). However, HP is known to alter the stability of proteins and can therefore affect the quality of salmon flesh. In this study, the effects of HP treatment for 5 min at 200, 400 and 600 MPa on the structure of Atlantic salmon were investigated. Transversal histological sections revealed a decrease in the fibre size from 200 MPa associated with an expansion of the extracellular spaces. Connective tissue was found to be modified from 400 MPa, resulting in an increase in its surface area. Fourier transform infrared (FT-IR) microspectroscopy revealed a reduction in the α-helix content and an increase in the aggregated β-sheet structure content with increasing pressure, reflecting a change in the secondary structure of proteins from 200 MPa.