The fabrication of chitosan (CH) biocomposite beads with variable copper (Cu2+) ion doping was achieved with a glutaraldehyde cross-linker (CL) through three distinct methods: (1) formation of CH beads was followed by imbibition of Cu(II) ions (CH-b-Cu) without CL; (2) cross-linking of the CH beads, followed by imbibition of Cu(II) ions (CH-b-CL-Cu); and (3) cross-linking of pristine CH, followed by bead formation with Cu(II) imbibing onto the beads (CH-CL-b-Cu). The biocomposites (CH-b-Cu, CH-b-CL-Cu, and CH-CL-b-Cu) were characterized via spectroscopy (FTIR, 13C solid NMR, XPS), SEM, TGA, equilibrium solvent swelling methods, and phosphate adsorption isotherms. The results reveal variable cross-linking and Cu(II) doping of the CH beads, in accordance with the step-wise design strategy. CH-CL-b-Cu exhibited the greatest pillaring of chitosan fibrils with greater cross-linking, along with low Cu(II) loading, reduced solvent swelling, and attenuated uptake of phosphate dianions. Equilibrium and kinetic uptake results at pH 8.5 and 295 K reveal that the non-CL Cu-imbibed beads (CH-b-Cu) display the highest affinity for phosphate (Qm = 133 ± 45 mg/g), in agreement with the highest loading of Cu(II) and enhanced water swelling. Regeneration studies demonstrated the sustainability and cost-effectiveness of Cu-imbibed chitosan beads for controlled phosphate removal, whilst maintaining over 80% regenerability across several adsorption–desorption cycles. This study offers a facile synthetic approach for controlled Cu2+ ion doping onto chitosan-based beads, enabling tailored phosphate oxyanion uptake from aqueous media by employing a sustainable polysaccharide biocomposite adsorbent for water remediation by mitigation of eutrophication.