Biorefinery of rubber tree side streams could add economic value and income for farmers, who already grow the trees for latex production. The objective of this research was to design a process for the recovery of proteinaceous fractions from rubber tree. The aimed applications were expected to be suitable for local use, particularly in Indonesia, being one of the world’s largest rubber producers. Rubber seed was selected as a model biomass based on its availability (21-144 kg-protein/ha) and its oil content that enables the combination of protein and biodiesel productions within a biorefinery framework. Experimental works were focused on three parts: separation of protein and oil from rubber seed kernel, enzymatic hydrolysis of rubber seed protein into amino acids, and separation of amino acids from hydrolysate. Using alkaline extraction, up to 80% protein from the total original amount of protein in the kernel could be recovered in the extract, comparable to protein recoveries from other oilseeds and oilseed cakes. Seed type and pre-treatment had the most influence on protein recovery. Following protein extraction, the extracted proteins were recovered via isoelectric precipitation, resulting in rubber seed protein concentrate that can be used as such or can be processed further. Different protease combinations were used to hydrolyse rubber seed protein concentrate. After 24 h hydrolysis of rubber seed protein, up to 53% degree of hydrolysis and 35% protein recovery as free amino acids could be achieved. Combination of Pronase + Peptidase R resulted in the highest recovery and concentration of hydrophobic amino acids (phenylalanine, leucine, isoleucine, tyrosine, tryptophan, valine, methionine, and proline) in the hydrolysate. Some hydrophobic amino acids are essential in human and farm animal diets, therefore they can potentially be applied as a group in food and feed. Ethanol was used as an anti-solvent for selective precipitation of amino acids. Ethanol was able to selectively increase the hydrophobic amino acid fraction in rubber seed protein hydrolysate from 59% (mol/mol) in the starting material to 76% in the supernatant. Leucine and valine contributed most to this increase. The results of this study show that rubber seed proteins can be applied locally as animal feed or in industries for technical applications.