Separation and purification processes of neutraceuticals, such as bioactive peptides, are usually done in a multistep process that sometimes requires a final chromatographic step using expensive resins. Activated carbon is a promising economic alternative for the resins. We report here on the application of a hydrophobic interaction on a chromatographic column packed with particles of activated carbon to isolate a lactotripeptide from a crude hydrolysate. Consecutive adsorptive–desorptive cycles were used until exhaustion of the column. Liquid chromatography–mass spectrometry results showed an enrichment of the lactotripeptide isoleucine–proline–proline with a yield of up to 80% in the third cycle and a twofold increase in purity to up to 35%. Some guidelines are given for the competitive exhaustion of the adsorbent for process optimization in order to obtain higher purity and yield.