An analytical methodology was developed for the first time in this work to investigate the peptide composition of coffee silverskin protein hydrolysates. Coffee silverskin is the only by-product produced in the coffee roasting process and it contains a relatively high amount of proteins (16.2–19.0%). Different extraction procedures were tested to obtain protein extracts from coffee silverskin samples which were subsequently submitted to enzymatic digestion using different enzymes. Protein hydrolysates from Arabica coffee silverskin obtained using three roasting degrees (light, medium and dark) were considered in order to evaluate the influence of this process on peptide composition. Antioxidant and hypocholesterolemic activities were investigated for these hydrolysates. A method based on the use of liquid chromatography coupled to a quadrupole-time-of-flight mass spectrometer was developed enabling the separation and identification of different short chain peptides in the coffee silverskin hydrolysates using de novo sequencing tool. Different peptides, with a number of amino acids ranging from 4 to 12, were identified in the coffee silverskin analyzed. Peptides obtained were different depending on the enzymatic hydrolysis employed. As general trend, the results obtained showed that peptide composition in coffee silverskin protein hydrolysates was not significantly affected by the coffee roasting process.