Poly(hydrophobic amino acids) have been utilized as a component of peptide-based vaccines due to their ability to act as an immunostimulating moiety. They are biodegradable, possess defined stereochemistry and number of units, and upon conjugation to peptide antigens can self-assemble into nanoparticles. However, the process of synthesis and purification of the conjugates presents notable difficulties due to the highly hydrophobic nature of poly(hydrophobic amino acids), resulting in low production yield. Herein we present a protocol for the optimized automated synthesis and purification of these conjugates.