Despite the early promises of magnetic hyperthermia (MH) as a method for treating cancer, it has been stagnating in the past decade. Some of the reasons for the low effectiveness of superparamagnetic nanoparticles (SPIONs) in MH treatments include (a) low uptake in cancer cells; (b) generation of reactive oxygen species that cause harm to the healthy cells; (c) undeveloped targeting potential; and (d) lack of temperature sensitivity between cancer cells and healthy cells. Here we show that healthy cells, including human mesenchymal stem cells (MSCs) and primary mouse kidney and lung fibroblasts, display an unfavorably increased uptake of SPIONs compared to human brain cancer cells (E297 and U87) and mouse osteosarcomas cells (K7M2). Hydroxyapatite (HAP), the mineral component of our bones, may offer a solution to this unfavorably selective SPION delivery. HAP nanoparticles are commended not only for their exceptional biocompatibility but also for the convenience of their use as an intracellular delivery agent. Here we demonstrate that dispersing SPIONs in HAP using a wet synthesis method could increase the uptake in cancer cells and minimize the risk to healthy cells. Specifically, HAP/SPION nanocomposites retain the superparamagnetic nature of SPIONs, increase the uptake ratio between U87 human brain cancer cells and human MSCs versus their SPION counterparts, reduce migration in a primary brain cancer spheroid model compared to the control, reduce brain cancer cell viability compared to the treatment with SPIONs alone, and retain the viability of healthy human MSCs. A functional synergy between the two components of the nanocomposites was established; as a result, the cancer versus healthy cell (U87/MSC) selectivity in terms of both the uptake and the toxicity was higher for the composite than for SPIONs or HAP alone, allowing it to be damaging to cancer cells and harmless to the healthy ones. The analysis of actin cytoskeleton order at the microscale revealed that healthy MSCs and primary cancer cells after the uptake of SPIONs display reduced and increased anisotropy in their cytoskeletal arrangement, respectively. In contrast, the uptake of SPION/HAP nanocomposites increased the cytoskeletal anisotropy of both the healthy MSCs and the primary cancer cells. In spite of the moderate specific magnetization of HAP/SPION nanohybrids, reaching 15 emu/g for the 28.6 wt % SPION-containing composite, the cancer cell treatment in an alternating magnetic field resulted in an intense hyperthermia effect that increased the temperature by ca. 1 °C per minute of exposure and reduced the cell population treated for 30 min by more than 50%, while leaving the control populations unharmed. These findings on nanocomposites of HAP and SPIONs may open a new avenue for cancer therapies that utilize MH.