Currently, marine macroalgae represent a significant biological and economic resource. Natural molecules derived from this biomass contain numerous bioactive compounds with high nutritional and pharmaceutical potential. Initially, we focused on the development of an efficient method for algal cell wall destruction and the release of proteins from two species of red macroalgae (Sphaerococcus coronopifolius and Gelidium spinosum). Pretreatment of these biomasses by ultrasonication for 60 min proved to be the most suitable technique for protein extraction. These proteins were then digested with pepsin (pH 3.5 and 40 °C) for 24 h to produce several protein hydrolysates enriched with bioactive peptides from S. coronopifolius and G. spinosum, namely SCPH and GSPH, respectively. The peptide profiles of SCPH and GSPH were subsequently analyzed by reverse-phase high-performance liquid chromatography–quadrupole-time-of-flight mass spectrometry (RP-HPLC-QTOF/MS), with MS data bioinformatics management. In silico analysis of the hydrophobicity and toxicity of the identified peptides were also determined. Furthermore, angiotensin conversion enzyme (ACE)- and Dipeptidyl-peptidase-IV (DPP-IV)-inhibitory peptides were predicted using a quantitative structure–activity relationship (QSAR) method. Both protein hydrolysates exhibited large heterogeneity regarding peptide composition. Peptidomic analysis allowed the identification of 172 and 64 unique peptides from SCPH and GSPH, respectively. Thus, 26 common peptides for both species were found. Additionally, both hydrolysates contain a large percentage of highly hydrophobic peptides (62.63% and 53.48%, respectively) and have a low molecular weight with no toxic effects. Furthermore, the identified peptides showed a high proportion of potent predicted ACE-inhibitory peptides (IC₅₀ < 100 μM), in the range of 59.88% and 81.53% for SCPH and GSPH, respectively. Moreover, the potent predicted DPP-IV-inhibitory peptides were quantified as 92.98% and 91.30% for SCPH and GSPH, respectively. These findings indicated that protein hydrolysates from these two red macroalgae present an attractive source of food-derived bioactive peptides with promising nutraceutical properties, especially antihypertensive and antidiabetic activities.