Herein we report for the first time the synthesis of three-dimensional scaffolds in the binary system SiO2–P2O5 exhibiting different scales of porosity: (i) highly ordered mesopores with diameters of ca. 4 nm; (ii) macropores with diameters in the 30–80 μm range with interconnections of ca. 2–4 and 8–9 μm; and (iii) ultra-large macropores of ca. 400 μm. The hierarchical porosity of the resulting scaffolds makes them suitable for bone tissue engineering applications. The chemical nature and mesoporosity of these matrices would allow these scaffolds to act as local controlled delivery systems of biologically active molecules, such as certain drugs to treat bone pathologies. The synthetic method consists of the combination of a single-step sol–gel route in the presence of a surfactant as the mesostructure directing agent and a biomacromolecular polymer such as methylcellulose as the macrostructure template followed by rapid prototyping technique. An exhaustive study of the aging process as well as of the rheological properties of the slurry after methylcellulose addition has been carried out to obtain hierarchical meso-macroporosity. This study allows the establishment of the time period in which the slurry presents appropriate viscosity to be extruded during the rapid prototyping once the ink is prepared. The setting up of this manufacture process at the laboratory level is important from the industrial point of view when the large-scale production of scaffolds for bone tissue repair and regeneration is targeted.