The assessment of enzymatic activity on Atlantic horse mackerel (Trachurus trachurus) during frozen storage was carried out in samples pre-treated by high-pressure processing (HPP) combinations of 150, 300 and 450 MPa with 0-, 2.5- and 5-min holding time (untreated samples were used as controls). The activities of four enzymes (acid phosphatase, cathepsins B and D, and lipase) in fish muscle were quantified during accelerated storage conditions (up to 3 months at −10 °C). The experimental data were fitted to second-order polynomial models to determine the effect of pressure level, holding time and frozen storage time on these enzyme activities and to identify conditions of maximum/minimal enzyme inactivation. Acid phosphatase and cathepsin (B and D) activities were significantly (p < 0.05) influenced by HPP, showing behaviours during frozen storage different from control samples. Acid phosphatase and cathepsin B activities decreased (p < 0.05) with HPP treatments, being this effect more intense for cathepsin B, particularly at 450 MPa. Regarding cathepsin D, the activity increased (p < 0.05) at intermediate pressure (300 MPa) and decreased (p < 0.05) at higher pressure (450 MPa). During frozen storage, cathepsin D enzymatic activity tended to increase over time indicating activity recovery of these enzymes. Although a predictive model for its activity was not acceptable, the increase in lipase activity during storage was the most pronounced trend observed.