Diclofenac sodium (DS) is an emergent pollutant, and among the methods investigated for its removal, adsorption is the most widely utilized technique. Hydroxyapatite and chitosan are biomaterials often used for adsorption. However, both biomaterials are limited due to their low chemical stability in an acidic medium; furthermore, pure hydroxyapatite interacts poorly with diclofenac. In this work, hydroxyapatite was organofunctionalized with 3-aminopropyltrimethoxysilane and further used to obtain amino hydroxyapatite /chitosan hybrids by crosslinking with glutaraldehyde at pH 3, 4, 5, and 6. X-ray diffraction patterns indicated the preservation of the hydroxyapatite phase under all pH conditions. Based on the control reaction of the amino hydroxyapatite with glutaraldehyde and its further reduction in sodium borohydride, the formation of CN moieties was highlighted as the main interaction mechanism between the aldehyde and amino groups. Therefore, crosslinking with glutaraldehyde was evaluated by infrared, Raman spectroscopy, and 13C NMR techniques; the results suggested contributions of imine formation and hydrogen bonding. The hybrid obtained at pH 3 exhibited an enhanced adsorption capacity of 125 mg g−1 at 15 min. The synergy between amino hydroxyapatite and chitosan crosslinked by glutaraldehyde was demonstrated.