The use of meat by-products as a potential source of protein hydrolysates rich in bioactive peptides is of growing interest to valorise these products and improve their sustainable use. This study aimed to evaluate the effect of different pre-treatments (hydrolysis with pepsin, ultrasounds, and ultrasounds-assisted pepsin hydrolysis) on the peptide profile and bioactivity of beef liver hydrolysed with flavourzyme. The pre-treatments with pepsin increased the degree of hydrolysis and generation of free amino acids in the liver hydrolysates, whereas the subsequent hydrolysis with flavourzyme influenced the molecular weight distribution of the peptides. Samples pre-treated with pepsin and ultrasounds-assisted pepsin hydrolysates showed the highest values of antioxidant and inhibitory activity of ACE-I, ECE-I, DPP-IV, and neprilysin enzymes, and therefore these hydrolysates were characterised to obtain the bioactive peptide profiles. A total of 995 peptides were identified by tandem mass spectrometry in the most active fractions separated by reversed-phase liquid chromatography, and 20 of them were predicted as potentially responsible for the observed bioactivities and subsequently characterised by in silico tools. These results evidenced the potential of hydrolysis pre-treatments with pepsin and ultrasounds-assisted pepsin to obtain beef liver hydrolysates rich in bioactive peptides that could exert multifunctional bioactivities such as antioxidant, antihypertensive, and antidiabetic, while giving added value to this meat by-product.