On the basis of a thermal process, a facile, low cost, one-step approach for preparing iron oxide (Fe₂O₃) incorporated ordered magnetic mesoporous silica nanocomposites by a co-operative self-assembly approach is presented. Various mesostructured silica materials incorporated with different amounts of iron oxide (nSi/nFe = 1/1, 1/0.5, 1/0.25 and 1/0.123) at various pH (<1, 3, 5 and 7) were synthesized and characterized by electron microscopy and X-ray diffractometry. Further, the surface area and magnetic properties were evaluated using N₂-sorption analyses, and a superconducting quantum interference device interfaced with a vibrating sample magnetometer (SQUID-VSM) respectively. The transmission electron micrographs and nitrogen sorption analysis indicated that most of the Fe₂O₃ domains of several nanometers were embedded in the silica walls, rather than dispersed in the mesopores. The incorporation of iron oxide into the mesopores without compromising the structural and textural properties was achieved at pH < 1. These structures have great potential in diagnostics and therapeutics. However, the acceptance of this material by the biological host is a critical issue for such biomedical applications. In this study, we have also evaluated the in vivo biocompatibility of these magnetic mesoporous materials in a rat model. The histopathological results show that this magnetic material can be classified as a level 2 biomaterial that can be safely used for short term applications such as MRI imaging, hyperthermia, targeted drug delivery, etc.