Valorisation of side-streams in food production has become an important booster for increased sustainability in food production. The objective of this work was to study and improve the functional properties of green coffee (GC) protein. Extraction of defatted GC meal by using PVPP slightly increased protein yield and significantly decreased the amount of covalently and non-covalently bound CQA, therefore decreasing the antioxidant activity of the meal. Peptic hydrolysis at pH 1.5 led to a significantly higher degree of hydrolysis (DH) than at pH 3. Sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE) showed that the molecular weights of peptides of GC protein hydrolysates were in the range of 11–60 kDa, while peptides were in the range of 500–5000 Da using matrix-assisted laser desorption/ionization-time of flight mass spectroscopy (MALDI-TOF MS). Additionally, the enzymatic hydrolysis significantly improved the antioxidant activity of the GC protein. Finally, the results suggest that enzymatic hydrolysis with pepsin is an effective technique to provide bioactive compounds. The works presented in our manuscript may help in further exploiting the potential use of green coffee beans for food, cosmetic or pharmaceutical industry.