The development of universal methods to synthesize materials with different structures is always in the researchers’ focus. Despite the fact that various structures based on magnetite have already been obtained, synthetic approaches that allow to synthesize materials with a wide range of texture and functional properties are still very poorly presented. In this work, we demonstrate that a stable magnetite hydrosol can be easily converted into monolithic structures of xero-, cryo- and aerogel by careful varying concentrations and drying conditions. We have also theoretically explained the observed effects by studying the percolation threshold at the sol–gel transition by means of controlled assembly of magnetite nanoparticles. At the calculated percolation point three types of materials different in porous organization were obtained. Due to the high biocompatibility of magnetite nanoparticles, the materials obtained were evaluated for cytotoxicity on HeLa cells line. All synthesized magnetite structures show excellent biocompatibility and minor cytotoxic effects at concentrations up to 1 µg mL−1. Considering that the porosity of materials can influence the manifestation of the hemostatic effect, whole-blood clotting study revealed the hemostatic potential of magnetite aerogel. That fact can be explained by presence spongy structure of the aerogel that allowed blood to be rapidly absorbed through full contact.