Multifunctional nanomaterials with controlled physicochemical structures can be advantageous for several therapeutic applications. In this study, mesoporous nanorods-like particles of cobalt doped hydroxyapatite (CoHAP, Ca10−xCox(PO4)6(OH)2) having varying concentrations of Co2+ ions were hydrothermally synthesized. Nanopowders (NPs) were comprehensively studied using XRD, Rietveld, FTIR, HRTEM, EDX, BET, VSM, and UV–VIS techniques. In addition to the structural and physicochemical properties; magnetic, induction-heating, drug loading, and releasing efficiencies followed by in-vitro bioactivity attributes were also explored. Results suggested that with increasing concentration of Co2+ ions; size and crystallinity of HAP crystals decreased, whereas, lattice strain, specific surface area, porosity, and saturation magnetization of nanorods-like mesoporous particles increased. HAP remained a chief phase with brushite as a secondary phase in CoHAP NPs. Furthermore, increased concentration of Co2+ ions contributed to the enhanced rise in temperature with increasing magnetic field and exposure time, suitable for hyperthermia applications. In addition, the drug loading efficiency of NPs increased with increasing concentration of Co2+ ions and also exhibited controlled drug release rate. In-vitro incubation of NPs for 30 days exhibited superior bioactivity with nucleation of bioresorbable secondary phases. Thus, the concoction of paramagnetism and induction-heating abilities with superior textural and bioactivity properties of NPs suggested their high potential for multiple applications, including tissue regeneration, hyperthermia anticancer treatment, and drug delivery systems.