In this study, the chitosan-based matrixes (granules and sponge) were synthesized and characterized as potential materials for protein purification from lipopolysaccharide (LPS) content. Two phage-borne enzymes with medical potential (endolysin 15 kDa and depolymerase 200 kDa) were used as model proteins for purification efficiency measurement. The endolysin purification by the chitosan-based matrix in granule form enables high protein recovery (99%) but with a low level of LPS removal (4%). In contrast, the sponge form exhibited higher efficacy in LPS elimination (64%) and it was accompanied by the loss of ∼28% of the endolysin content. The LPS removal from depolymerase samples was similar for both matrixes forms at the levels of 72% and 78% with a superior capacity over commercially available endotoxin removal resin (62%). The active depolymerase recovery was around 89% and 76% for granules and sponges, respectively. No proteolytic effect and a slight decrease in enzyme activity were observed. In conclusion, the purification efficiency of chitosan-based matrixes from LPS was dependent on the morphology of the matrixes but not on the size of the protein. Our study proved that chitosan-based matrixes are attractive options for recombinant protein pre-clean purposes.