Adsorption processes using a packed bed reactor are often used for the purification of nutraceuticals. However, when dealing with untreated streams, this leads to fouling and consequent increase in pressure drop. This work compares the use of channeled monoliths, "honeycomb" structures, with a packed bed, both made of the same type of activated carbon. The intrinsic permeability and performance of both structures during the adsorption of a bioactive peptide from a crude hydrolyzate were studied. Breakthrough experiments were performed on both types of systems under similar conditions. The results showed similar productivity and dynamic adsorptive capacity for both structures at comparable linear velocity and residence time, but the packed bed showed a strong pressure drop increase during column saturation, revealing plugging of the column, especially at high velocities (short residence times). The channeled monoliths did not present any significant pressure drop increase, and were able to operate at high velocities which increase the range of application for these types of processes.