Congo red (CR) is a stable anionic diazo dye that causes allergic reactions with carcinogenic properties. The rapid removal of CR using cation-incorporated nanohydroxyapatite (pristine HAp: X (X = Fe, Ni, Zn, Co, and Ag)) was investigated. The pristine and cation ion-doped HAp adsorbents were coprecipitated and subjected to hydrothermal and ultrasound treatments and subsequent microwave drying. The dopant ions significantly engineered the crystallite size, crystallinity, particle size (decreased 38–77%), shape (a rod to sphere modification by the incorporation of Ag+, Ni2+, and Co2+ ions), and colloidal stability (CS) of the adsorbent. These modifications aided in the rapid removal of the CR dye (98%) within one minute, and the CR adsorption rate was found to be significantly higher (93–99%) compared to previously reported rates. Furthermore, the kinetic, Langmuir, Freundlich, and DKR isotherms and thermodynamic results confirmed that the CR adsorption on the HAp was due to the strong chemical adsorption process. The order of the maximum CR adsorption capacity was Fe-HAp > HAp > Ag-HAp > Co-HAp > Zn-HAp. Whereas the CR regeneration efficiency was Fe-HAp (92%) > Ag-HAp (42%) > Ni-HAp (30%), with the other adsorbents exhibiting a poor recycling efficiency (1–16%). These results reveal Fe-HAp as a potential adsorbent for removing CR without the formation of byproducts.