Selective ion incorporation into the milkfish (Chanos chanos) bone-extracted hydroxyapatite (HAp) structure paves way for value-added end-of-life application and regulated ion species doping. High purity (99.7%) HAp with Ca/P ratio of 1.58 is extracted from waste milkfish bones via thermal treatment and subjected to concentration-varied aqueous-facilitated binary cupric ion (Cu2+)/zinc ion (Zn2+) system doping. Thermogravimetry describes the thermal behavior of milkfish bones prior to HAp extraction with three decomposition stages. Scanning electron microscopy-energy dispersive x-ray spectroscopy (SEM-EDX) shows the similar particle morphology of HAp and the varying Ca/P ratio for all samples. X-ray diffractometry (XRD) confirms the identities of HAp and calcite impurity (0.3%) and shifts in the (211), (112), and (300) peaks after ion doping. Results reveal that selective substitutional doping of Cu2+ into the HAp structure—displacing calcium ions (Ca2+)—occurs in a binary Cu2+/Zn2+ system as signified by decreased lattice parameters, altered Ca/P ratio with respect to undoped HAp as attributed to the detected copper, undetected zinc, and increased microstrains after doping. The crystallite size and crystallinity are determined to increase as the Cu2+ concentration is increased among the ion-doped HAp. Implications of the Cu2+ doping of HAp highlight its potential for applications such as, but not limited to, cation sequestration and antibacterial systems.